Some or all of the below information will be requested if it isn’t supplied; for fastest response please provide as much as you can. 
The Basics
- Nextcloud Server version (e.g., 29.x.x):
31.0.4 - Operating system and version (e.g., Ubuntu 24.04):
Ubuntu 20.04.6 LTS - Web server and version (e.g, Apache 2.4.25):
nginx/1.18.0 (Ubuntu) - Reverse proxy and version _(e.g. nginx 1.27.2)
none - PHP version (e.g, 8.3):
8.1 - Is this the first time you’ve seen this error? (Yes / No):
Yes - When did this problem seem to first start?
After update - Installation method (e.g. AlO, NCP, Bare Metal/Archive, etc.)
Downloaded archive - Are you using CloudfIare, mod_security, or similar? (Yes / No)
No
Summary of the issue you are facing:
After the update, I noticed some strange behavior with the uploaded files.
The built-in file manager shows that the files were changed more than 2 months ago, but the OS filesystem itself shows only today’s timestamps.
Did I do something wrong during the last upgrade?