Deleted file became system data, that now doesn't exist in finder and cannot be deleted

1kysymys wrote:

This didn’t happen today though, it has been system data for months now.

Perhaps there is something funky with your local snapshots. You can view them in Disk Utility. Use the "View" menu to "Show APFS snapshots". You will also have to right click on the column headers and show all of the sizes. It is one of the non-default columns that actually shows how much space the snapshot is taking. I don't have any snapshots on this machine so I don't remember which column it is. I just know it isn't one of the default ones.

Once you find the offending snapshot, you can use this interface to manually delete it. Or you can just delete all of them.

It is generally a good computer practice to alway keep at least 20% to 25% of the Total Drive Capacity’s as Empty Space.

Allowing the computer to drop below these guidelines may eventually, cause unintended consequences.

There is Purgeable Space and there is Empty Space.

As previously mentioned, Purgeable Space which is Controlled by the Operating System.

When the Operating Systems decides the computer needs additional Empty Space, it will move a portion of the Purgeable to Empty space

AFAIK - there is no User Actions to hasten this transition from Purgeable to Empty Space

It can day or longer before this will occur.

The links below will assist in identifying what is taking up space on the Internal Drive and provide possible ways to remove data that is under the direct control of the User ( Home Folder ) . 

Rebuild the Spotlight index on your Mac

What is “Other” storage on a Mac, and how can I clean it out?

Free up storage space on your Mac

GrandPerspective 

How to delete Time Machine snapshots on your Mac.  

Often caused if the Time Machine Drive has not been attached  to the computer and TM Backup is set to run on a Schedule. 

TM Backup will make Snap Shot on the Internal Drive awaiting the TM Backup Drive to be attached. 

Only then will the Snaps Shots be transferred to the External Drive and deleted the Internal Drive.

See used and available storage space on your Mac

Locate backups of your iPhone, iPad, and iPod touch

Is there a Suite of Adobe Applications  used on this computer ?

They may create some very large cache files that can be removed. Though, the Adobe cache files will be recreated as the Applications needs them.

https://helpx.adobe.com/ca/premiere-pro/kb/clear-cache.html

The final word from Apple on Managing the " Other/ System Data “ Category

Other / System Data: Contains files that don’t fall into the categories listed here. This category primarily includes files and data used by the system, such as log files, caches, VM files, and other runtime system resources. Also included are temporary files, fonts, app support files, and plug-ins.

You can't manage the contents of this category.

The contents are managed by macOS, and the category varies in size depending on the current state of your Mac.

If you are sure the storage became System Data, then you need to have the "Data" volume selected on the left pane of Disk Utility before you will see the "Show APFS Snapshots" on the Disk Utility "View" menu. See this Apple article for details:

View APFS snapshots in Disk Utility on Mac - Apple Support

If you copied those files to another location on the APFS volume, or imported those items into Photos from pictures already stored elsewhere within home user folder, then the data was not deleted...you only deleted a small link to the data. File copies on APFS volumes keeps only a single copy of the data on the APFS volume and only adds links to the existing data. This is a feature of the APFS file system to help keep data usage low and to lower the rate of wear on an SSD. To delete data completely, you need to make sure to delete all "copies" of the data (or rather all links to it).

The paid versions of Daisy Disk can reduce Purgeable. No idea if other similar apps will do the same.

This is how it works. It will be purged within 24 hours. It shouldn't be slowing down your system any, at least not unless you are totally out of free storage space.

I also am having this issue and has nothing to do with snapshots or the trash can. Every single deleted file, app or anything goes directly to the system data. I have run repairs in system restore which are successful on the OS portion but fails on the Data portion. My System Data was at 125GB and then yesterday I deleted a photos library that was 209GB and now the System Data sits at over 230GB. All that data went directly to the System Data and I cannot find it anywhere to clear. I have cleared out the caches and logs, run maint scripts, turned off Time Machine and unplugged, check for snapshots (dont exist) and every single recommendation I came across from many google searches.

This really feels like some sort of bug and I would really like to at least update the OS to see if it helps, but the System Data has taken up 99% of my hard drive and I have no space to actually do the update.

Generally I do not reply to secondary questions from Other Users

That is done because it gets confusing as to Who the Owner of this question is.

Will just suggest re-reading the pervious posting and follow the suggestion as the Were the Space is being used and how to find it and remove it

The System Data “ Category

You can't manage the contents of this category.

The contents are managed by macOS, and the category varies in size depending on the current state of your Mac.