Hello, I'd like to tell you what has been happening with my system ever since the 15.3 update. It's similar to yours, but more alarming.
The day the update came out, I checked my storage after seeing reports of Apple Intelligence taking up a few extra gigabytes of space. I was using 167 out of 494GB. Once the update was done, It said it was using about 20GB less space. Very strange, but I didn't think much of it. I went to the settings and turned off Apple Intelligence. The usage dropped another few gigabytes, but then I noticed something very odd: The amount purgeable was the same as the amount used. After a couple of hours, programs started having errors and then I noticed my files were being corrupted. I checked my storage again and it was down to less than 100GB used and storage overview software (TrashMe 3 in my case) confirmed that a huge amount of data was gone. Restarting only made things worse.
I finally decided to completely wipe my internal drive and restore a recent Time Machine backup. That worked for a few minutes, but then the storage started calculating wrong again and the same thing happened.
I wiped the system again and didn't restore from Time Machine. I manually redownloaded all of my programs, activated them, configured macOS to roughly how it was. All seemed fine... until I started redownloading Steam games. It got to about 80GB downloaded when the storage information in Settings messed up again. It doesn't seem to be deleting files this time and isn't reporting any space as purgeable, but it's clearly wrong. It says I'm currently using 19.66GB when the application size being reported is 25.16 alone. System Data is continuously calculating. First Aid through the Disk Utility doesn't work on either a volume level or partition level. Everything comes back as normal. This has to be a bug in the 15.3 update.
I will reply again if files start disappearing again.
Edit: I forgot to say I'm on a 2021 M1 Pro MacBook Pro.