Not that I have the exact same issues you have, but I share your frustration with iCloud Drive. I have 2 TB space in my iClud Drine and is using 600 GB ... 442 for "Drive", 60 GB for "Messages" and 29.145 items for images ... I must assume the 29.145 items equals approximately 100 GB to make the numbers meet ... 

But my issue is another, and it started with it started with Messages … 

Wednesday morning September 10, I touched the spacebar to wake my Mac from sleep and checked my mail. While doing that my phone told med I had received a Message (are they still called iMessage?) and when i wanted to respond to it, I noticed Messages wasn’t running on my Mac, which was weird, because it always is. I type most of my messages on the Mac. 

So I found Messages in the dock, clicked it and was asked to sign in. That was unusual, I never have to do that, since I use it all the time. 

But I typed my Apple ID and my password and it logged me in as expected - except I did not see the new message I was planning to respond to. And after 15 seconds the Messages window disappeared and the Messages login window appeared again. I tried numerous time, but never got it to work. 

So I restarted and tried aganin. No luck. 

Annoyed I went to my workshop and opened the old computer I have there … a 2015 MBP with Monterey, and it was exactly the same. It had also logged itself out of Messages, and I could not log in. 

So, probably not a computer related issue, right? 

I called Apple, and I have at this time talked to 7 advisors.

The first one suggested it was the connection from my computer to iCloud, and I could solve it by logging out of iCloud and wait a few minutes and then log back in. 

Now, logging out of iCloud is not something you just do, when you also use iCloud Drive and Calendar and whathaveyou. It takes time, and I have had problems with it before back in January. 

I have to say, at this point, that I don't have Optimize Mac Storage enabled, so I have all my folders and files in “full size" on my computer. In other words, it should not take long to log in and start working. 

So I did it to try to solve the Messages issue. 

And I shouldn’t have. Big mistake. 

It looked like my comuter started downloading everything again, and my folders - and most subfolders - in Desktop and Documents suddenly had 10 September2025 as their Modified Date, which makes it impossible to sort folders by Date Modified, which is what I usually have. So my "navigation system” is f**** up.

I now also have a iCloud Drive (Archive) folder in my user folder .... with some, but far from all, the folders from iCloud Drive. These folders too have 10 September 2015 as their "Date Modified"

Another effect is, that Time Machine seems to view my files as new og changed, so the first time it ran after the log out/log in thing it started to do a full backup of everything. 

An Messages still don’t work. 

Obviously there is no way to get the dates on the folders back to what they were, eventually with time as I edit og save stuff in those folders, the date will again change to the Date Modified, but until then I’m stuck with September 10 2025.

I have talked to Apple Support several times, and they have absolutely no idea! 

Two different supportes informed me, that dates are considered meta-data and meta-data is not transferred to iCloud. Which is a horrible thing to say since my files have the correct date … it’s just the folders that have had their dates changed. 

And to make it even more strange: It’s not all of them. Some of the folders and subfolders have the correct date. Duh! How ? And some still have 10 January 2025 - which was the last time I had “iCloud trouble” and a “Senior Advisor” told me it could be fixed by logging out and back in again. So yes, I have been here before, and i was worried, but I needed to get the Messages issue fixed. This time I told the advisor about my earlier experience, and during a screen sharing session he checked my iCloud Drive settings and said not to worry, “that will not happen, since you already have all your files on your computer”.

Well, it did.  

So ...

Why does this happen? 
Why is it only folders and subfolders but not files, that have the Date Modified changed? 
Why is it not either or? Why did 36 of my 59 folders in Documents have the date modified to 10 September 2025 and 23 still have 10 January 2025 as the Date Modified? 

So I called Apple again, and Apple don’t know. My issue was again escalated to Senior Support and I was again told that Apple consider Date Modified as meta-data and meta-data is not transferred to iCloud Drive, so when you download folders from iCloud Drive, the date Modified will be the download date. 

That is not true! 

Parallel to this, I have been helping a friend, who had his comuter stolen. We bought him a used but very nice MacBook Air 15” M2, reformatted the SSD, installed Sequoia, typed in his Apple ID and password and his files and folders were downloaded from iCloud Drive. With the correct Date Modified dates! 

So why is this happening to me? I have never experienced this on my old computer - and have logged out and in of iCloud several times. I have only experienced this mess with this computer.

So I ask … has any of you experienced this Date Modified issue if you have had to log out of iCloud and back in? Or is it just me? 

And btw … Messages still don’t work, so I have to call Apple support again today. Sigh!: