Nextcloud version : I faced the same issue on different nextcloud instances
Operating system and version : idem
The issue you are facing:
At least for 4 times in the past, I faced the following issue (the last one was today) :
Several users started to tell me (the nextcloud administrator) that “their” files/directory are disappearing !
Of course, they were doing noting special (on these files).
Each time, the only clue I had (but can’t and don’t want to check/test if I’m right or wrong) is the following :
As administrator of nextcloud servers, I usually have a client connected as admin. Where I faced the previously mentioned issue, I have to say that a few minutes or hours before, I had my / (or /usr) full because of some admin action on my computer (like you know, dist-upgrade 
It appears to me that if there is no more space on “system” partition, nextcloud client may(?) start to behave crazy… (deleting stuff randomly).
Is this the first time you’ve seen this error? (Y/N): No
Steps to replicate it: (may be not easy to replicate)
- Doing things that may full the / or /usr partition (e.g. apt upgrade
- Nextcloud client, logged as Admin on the server starts to delete files/directory randomly
NB : Today, after cleaning the system and giving me free (sytem) space, the client starts (magically) to restore the deleted files ! I’m lucky this time.