I updated to the 12.3 beta the other day (by accident, I didn't realize or know how I ended up in the beta program for Mac), and I realized my Documents folder was empty. I thought perhaps it is a visual glitch and put another file in there, then rebooted, and that file is now missing too on reboot. Spotlight and Finder can't find any of the missing files so I believe they're being deleted on reboot now. Hope this is fixed soon.
macOS 12.3 erasing documents folder on boot
Hello, have you checked if the Documents directory appears on your iCloud?
The situation you say seems a lot similar to when you let iCloud Drive store the Documents and Desktop files on the cloud.
Cheers, Franz