Unlink all machines syncing with OD. Check the name that appears in the “Deleted by” column in the recycle bin then had this user unlink his/her account from all the devices and then try to sync afterwards. If there are multiple devices, then you have to do the try to sync it one at a time with a few hours of observation to learn which device is causing it.
Check what\who deleted the file in SharePoint logs. The article describe some steps on how to take advantage of SPO native tools on how to deal with missing or deleted files.
Consider creating alerts. This is one way to pin point the problem as from this point you will be able to first hand witness who and what actor is accidentally or deliberately deleting these files.