Pls. Do this test. I have googled a lot and haven’t found answers on this odd bug. 
Open Disk Utility. Run first aid, repair if have to. Open finder. Tell me did your files, folders disappeared or part of them. Don’t scare if so. Just restarted Mac. It will “fix” the bug. Don’t forget to tell have you FileVault enabled.
Open Disk Utility. Run first aid, repair if have to. Open finder. Tell me did your files, folders disappeared or part of them. Don’t scare if so. Just restarted Mac. It will “fix” the bug. Don’t forget to tell have you FileVault enabled.