Your not the first to post about this, seems to be a similar thread every few months (example https://www.reddit.com/r/sharepoint/comments/wvpurq/files_deleted_by_sharepoint_app/)

Short version is its usually a user or system OneDrive sync app misbehaving and it has to be reset/reinstalled.

I've seen some where the CSC cache was corrupt on the system and that problem was the root cause of OneDrive locally registering the file as missing, also a failing SSD causing it and just straight up messed up OneDrive installs causing it.

Unfortunately the logging won't tell you which system is behind it typically so its a case of searching for a system with OneDrive sync that is missing that file in their local copy usually.