Macintosh HD Storage Incorrectly Reading as Full, Which is Causing Problems

Here's the update (in two parts, because I went over the character limit):

I found the external drive that I'd used for Time Machine back-ups in the past and checked out the most recent back-up, from early 2022 or so. To my happy surprise, some of the items that disappeared from the local mac and iCloud last week were from that time/earlier, so I was able to recover a few things. However, the external drive was not formatted as APFS, which Apple recommends for Time Machine back-ups, and my attempts to partition the remaining free space and reformat that using Disk Utility were unsuccessful.

I went to my other external drive, the one that I'd been using recently to save movies and TV shows onto, which was formatted as Mac OS Extended (Journal). I partitioned 2 TB (just over twice the size of my mac's storage capacity, which is what the internet recommended) of free space and reformatted that to APFS. Then, I backed up everything on Time Machine. I followed the instructions of erasing the mac and restoring it to factory settings (or, as I described it to others, nuking the laptop), started it back up, and used Migration Assistance to bring everything from the Time Machine back-up over.

I was honestly a bit surprised as to just how much was saved by the back-up, and it turns out that my concern of the back-up also containing the remnants of CleanMyMac and anything else that had caused this problem in the first place was well-founded, considering that I found files containing those relevant keywords when I searched them up in Finder and got this somewhat concerning report from EtreCheck:

I reviewed what I could, deleted the files and other items it recommended, but it still wasn't enough:

So, I started the process of backing everything up on Time Machine and nuking the laptop all over again. I rebooted the device and downloaded EtreCheck just to check that everything was alright to begin with:

This time, I opened up the most recent Time Machine back-up (I didn't go into Time Machine itself, but into the files on the external drive connected to the laptop) and systematically started dragging items that I recognized from there into local Finder windows. (I initially tried to just copy the two main folders on the back-up's desktop, except they only copied a few thousand items each instead of the tens of thousands of items that they actually contained, so I ended up copying the contents of each folder and subfolder into new ones on the local desktop.)

My computer wasn't really thrilled about this and quickly started heating up. I used EtreCheck at least twice during this process and got these reports:

My process may have screwed up some of my transferred applications, such as Google Chrome and Spotify. Regarding the first one, I attempted to open the app repeatedly, except it just bounced instead. I deleted everything containing the keyword "Chrome" in Finder and tried to reinstall the app from the website, but no luck. I restarted my laptop and tried again, still nothing. I couldn't find it in the App Store when I searched it up, so I went through the website and it brought me to Chrome on the App Store, but it wouldn't let me download the app and just said "Not compatible with this device. See full list of compatible devices." Computers were not on the list of compatible devices. Which, weird. Because 24 hours ago, I had and was able to use Chrome on this very laptop. The same thing happened with Spotify, where it just kept bouncing and finally stopped after a while. I deleted the app, tried reinstalling—basically the same thing as with Chrome (the App Store gave the "Not compatible with this device." message again), except I didn't delete anything other than the app itself. It's kind of working now? It takes longer than usual to open the app, but at least it's opening. Another example is Preview, which won't open when I double-click on an item. That one is going to become problematic real fast.

The other apps are working without any issues so far that I've noticed. I think it's more the fact that I haven't used them to their full extent enough to notice problems, considering that I thought Safari was fine until I tried inserting an image to this post, then the app froze completely and I got the beachballing rainbow circle of doom. That was fun! Same with System Settings, where everything has worked normally, except for trying to change the wallpaper. I use a photo that I keep on my desktop and I kept quitting and reopening, then restarting entirely and reopening, the app over and over again just to open "Add Photo," then move to the desktop tab, and finally select the photo in question. I finally succeeded, but it took a very long time.

Here's what I got:

A couple of hours after I posted the discussion above, I checked my System Settings again, and saw that it had reverted to this:

I'm willing to bet that's more or less how it was before everything started going weird.

Except there's another problem now. I mentioned above that the local files on my desktop are out of date, and the screenshot from the iCloud folder shows several folders for desktop, downloads, documents, etc., instead of just one each. I'm not sure what happened or where it started, but a lot of files, documents, photos, etc. that composed the 78,000+ (yes, I know that that's a lot) items on my desktop have disappeared. I currently have 60,000 items in the local desktop folder and it's decreasing with every second. And less than 3,000 items in the iCloud desktop folder.

It seems that there are more items on the iCloud website, and I've been trying to download everything, except it's really slow-going. They're not in the trash or anywhere else that I can find. I know that it's not the end of the world, but the accumulation/collection of these items is something that I've spent over 6 years on. I have so many folders and items that I don't even know what's missing or from where. And regaining every item from the source is unlikely, impossible, a waste of time... I just don't even know where to start.

And no, I don't have a back-up of everything on another drive. I, rather foolishly in retrospect, thought that keeping everything on iCloud was safe enough.

I downloaded the app and ran it under a couple of different reasons. Here's what I got:

I also did Tools>Storage and got this:

Also, some more details on this... purge, of sorts, that's affecting my laptop:

When I go to the iCloud folder in my Finder sidebar, this is what I see (picture below). Clicking "Desktop" brings me to "Desktop — iCloud," the greyed-out "Desktop 2" brings me to "Desktop — Local," and the "Documents" with the same icon on it as "Desktop 2" also brings me to "Desktop — Local." The "Documents" with no icon on it brings me to "Documents — iCloud," and "Downloads" just brings me to "Downloads," but it's not the local downloads folder (also called "Downloads"), because there's nothing in this one versus several items in the local one.

I'm not sure what, if anything, I can delete. (Though I've already removed several folders that appeared empty or like duplicates. See the last picture on the original post to get a sense of how many folders there used to be versus now.) "Desktop 2" and the "Documents" with the same icon on it both lead to the same place, so can I delete one of them? If so, which one?

All of the subfolders in the first "Desktop" folder are empty, but I've been checking and re-checking them every so often, and sometimes, new items, presumably from iCloud, are in there, which I then drag into the subfolders on my local desktop. I now have nearly 63,000 items on my local desktop.

I went back to the iCloud website drive, and all of the subfolders on there are now empty. I imagine that that's because of how I've been moving everything in the subfolders of the iCloud drive via Finder into the subfolders of the local desktop. However, I find this very alarming, because there were a lot of items in the iCloud website drive last night, and I was slowly downloading them onto the local desktop. And now they're gone. I'm not familiar with this, I don't know the technical terms, but it seems like I've just lost nearly 20,000 files on both the local laptop and iCloud because the local laptop was missing them, synced up with iCloud, and deleted them off of there too.

I don't know whether I should go to System Settings, disconnect my local files from the iCloud, and then reconnect them to resync them with the iCloud. I'm not sure what steps to take here just to return to some kind of normal and I am so scared that I will mess this up and lose everything. I don't even know if it's safe to reconnect the external drive that I've been keeping movies and shows on.

I haven't used Time Machine in years, same with back-ups on an external hard drive.... is there anything at all that I can do to bring my laptop's contents to what it was just 24 hours ago? I'm not new to losing items like this, but it's still devastating every time. I seriously have a curse, though. Every year, every single year, something happens to one of my devices, especially my laptop. Last year it was the screen shattering as I was about to take a test because it closed on top of a pencil I'd left on the keyboard. (I got it replaced and proceeded to crack the bezel only days later.) One time it just died during the night and wouldn't wake up no matter what I tried, and the Genius Bar couldn't figure out why. Another time I was caught in a flash summer storm and it drowned. I didn't back things up, either on an external drive or iCloud, back then and lost everything. Not to mention dropping my phone on gravel, screen face-down, causing it to shatter. Or being punched at (accidentally) in PE and my phone receiving the blow and shattering again. One of those times, I hadn't backed up my device in months and lost stuff again. My mom calls me the Apple Product Serial Destroyer/Killer. I've even been waiting for something to happen in the last few weeks. But this... I thought I was at least somewhat safe with iCloud. I didn't expect this to happen.

Both of those responses are a) rather terrifying, and b) definitely not what I was hoping to hear.

So this isn't a one-time thing where the computer glitched and a lot of items got lost forever, but at least it's over and won't happen again? There are still problems going on? What happened on Thursday could happen again, and worse???

Honestly, at this point, I can accept not knowing what happened or why if it means it not happening again. An explanation would be great, because then I'd know what not to do again in the future, but I can live without it if I have to. But I really, really don't want to go through losing more items. A lot of the missing photos, screenshots, downloads, etc. were collected more recently compared to the rest, so I have a pretty good idea of how much time I spent saving those, . The fact that I could still lose more.... please, no.

Regarding the reply about CleanMyMac, it's an application that I used many years ago and have since deleted. I looked it up in Finder and only found the EtreCheck reports and one .json file from 2022. It does seem to still have some features/permissions in System Settings, though. From what I remember, removing it was a bit of a pain, and I might've used another app (AppCleaner) to do so.

I've been thinking about what happened earlier that day (Thursday) and I realized that it may have had some impact/be of some relevance. Long story short, I kind of slipped and fell down the stairs getting to class. My laptop was in my backpack, which bumped down the stairs along with me, but I didn't notice anything wrong with it when I finally did get to class. Later that day, I attempted to download some films using MovPilot and a Canadian VPN (because Netflix Canada has some content that Netflix USA does not). However, they all kept failing to complete when nearly done (I'm talking 98, 99% downloaded). I had the audio and visual in separate files, along with more items like the subtitles, but not the actual final product that combined everything. I jumped from Toronto to Vancouver to Montréal over and over again, tried removing the films from the download list and downloading them in different orders, but nothing was working. This hadn't really happened before. Finally, I moved on. I hopped around a dozen different VPN countries (mainly Northern Europe and Eastern Asia) looking for other specific titles, and was finally successful with a Japanese VPN. I tried downloading some movies from there, but experienced a lot of slow downloading, failing at the last minute, and finally just received the warning that I mentioned in the original post, which was that I had insufficient storage to download the film at the top of the list. Then everything I've already mentioned happened.

[Edited by Moderator]

I'm sorry for starting my previous response with a facetious comment. Obviously I'm grateful for any and all help regarding this issue, especially if it means getting to the bottom of what happened and making sure that it doesn't happen again. And I'm even more grateful knowing that this is a community of volunteers who just want to help. So thank you for all the responses I've received so far.

To clarify a few things, since I want to make sure that I'm doing this right:

• When creating the Time Machine back-up, should I use a different external hard drive than the one I've been moving all the downloaded movies and shows to? And regarding that hard drive, given that it was attached to the laptop when all of this started, is it safe to ever attach again? What about accessing the contents on there? Are those safe to open?

• When creating the Time Machine back-up, will it also back-up the remnants of CleanMyMac? What about the other concerns mentioned, from malware to malicious content?

• Regarding the "don't install junk" comment, does this mean that I should not back-up/re-download apps such as Malwarebytes, ClearPass OnGuard, NordVPN, AppCleaner, etc.? The first two are required to be able to access my university's WiFi. And the third one has proven useful in so many instances. (Don't worry, I'm definitely never downloading CleanMyMac again.)

• What about browser extensions, from ad blockers to other useful ones such as OneTab and GoFullPage?

• Will the Time Machine back-up save browsing information, from my bookmarks, reading list, etc. to tab groups? Because I have a lot of tab groups with many tabs in them. If not, what's your recommendation for saving those?

• What personalized (for lack of a better term) information/content/items will the Time Machine back-up not back-up? So that I can save those in some other way/form.

• As for everything else, what do they mean and why are they problematic? Such as the system modifications in the background or orphan files that could be removed? Or the unsigned software files? What are those referring to? Why are they bad? As for having more than one antivirus app and a VPN app, how are those causing issues? Why are they not recommended? As for proxies, aren't those good? Basically, these were pointed out by EtreCheck as concerns, but why? What parts of them? How do I fix that and keep it from happening again?

• All I have to do is follow the steps here (Time Machine back-up) and here (erasing and resetting the Mac), and all will be good? I just want to be sure, because, not gonna lie, I'm a bit scared. This all seems very permanent, especially if I do something wrong even by accident.

Once again, thank you for everything you two have posted thus far. I appreciate all of the help and will listen to your recommendations. (I just have to write an essay first. It's already overdue because I've been focusing on this. Then I'll do all of the above and report back with the results.)

Could it have anything to do with Caches? Because I was directed there after scrolling through the Spotify forums and I noticed that it only has six folders, three of which have the red circle with the horizontal white dash in the bottom right corner, which means that I don't have permission to access them. I'd embed a screenshot, except that's not working right now, so I'll just write their names here:

• ColorSync
• com.apple.amsengagementd.classicdatavault
• com.apple.aned (I don't have access to this one)
• com.apple.aneuserd (I don't have access to this one)
• com.apple.iconservices.store (I don't have access to this one)
• Desktop Pictures

I checked the Caches in both my external drive and Time Machine, and came up empty. There is absolutely nothing there.

Also, here are the EtreCheck reports that I've generated since last night, when I realized that things hadn't gone as smoothly as I'd hoped for:

In short, I've got as many items as I could save when this whole fiasco started on my mac's desktop, backed-up in iCloud, and backed-up in Time Machine via an external drive. And I'm not seeing anything related whatsoever to CleanMyMac or the other suspicious items that EtreCheck had flagged before the most recent nuking of the laptop. So that's the good news. The bad news is that I've got at least several apps that are doing everything from some elements not working/working very, very slowly to just not opening at all. Which is not ideal.

Even EtreCheck is having problems! It works fine until I try closing the report, at which point it just freezes and I have to force-quit the application by pressing hard on its icon on the dock.

One thing I just realized is that I can move items from my downloads to the trash, but not from either my desktop or my documents. Those latter two are synced to iCloud. And currently, my laptop is trying to upload over 60,000 items to iCloud. That number doesn't match up perfectly with the 75,000+ items that I have in my desktop and documents combined, but could this have something to do with whatever is going on now? Or is it a separate issue? (Edit, from when I was typing up the numbers from Disk Utility: the items in my desktop and documents that I tried to put in the trash are now there, though I got two warnings around the same time that "The operation can’t be completed right now because another operation is in progress, such as moving or copying an item or emptying the Trash." I'm not sure what that's about.)

I'm also looking at my laptop's storage right now, since that's where this all started a week ago (literally, almost to the hour), and it won't load in System Settings. It just tells me that macOS is 19.02 GB, but everything else is spinning and "Calculating." At the top, though, it says that 180.98 GB is currently being used. (Edit, same thing as directly above: The numbers loaded. iCloud Drive is taking up 99.8 GB, Applications is taking up 62.68 GB, Messages is taking up 17.95 GB, and after that, the numbers get real small. Which is rather different from what my storage looked like several days ago, when over 600 GB had been used up. This whole thing is just baffling to me.)

I'm also looking at Disk Utility, where "Macintosh HD" (APFS Volume Group - APFS | 286.07 GB Used, 7.25 Other Volumes, 701.34 GB Free) splits into a greyed-out "Macintosh HD" (APFS System Volume - APFS | System Snapshot Mounted, Mount Point: Not Mounted, 994.66 GB Capacity, Zero KB Available, -- Used) and a not-greyed-out "Macintosh HD - Data" (APFS Data Volume - APFS | 275.85 GB Used, 17.49 Other Volumes, 701.24 GB Free AND ALSO 820.86 GB Available (119.62 GB Purgeable)). The greyed-out "Macintosh HD" also has a not-greyed-out sub-item, "Macintosh HD" (APFS Startup Snapshot - APFS | 10.24 GB Used, 283.19 GB Other Volumes, 701.24 GB Free).

These numbers or where they come from barely make sense to me, but maybe they'll mean something to someone else. And I'm really sorry about the formatting—I'd include screenshots if I could.

Also, since why not at this point, here's an EtreCheck report from just now:

At this point I'm genuinely considering wiping the computer and starting all over again, this time just bringing over the items in my desktop, downloads, and documents, and redownloading all of my apps from the App Store or their websites, if it means things just working as they should. But I really, really can't lose another day (or more) to this. I've already put everything else aside for too long.