I wonder if it's something like this:
- Client 1: Note 1 is created
- Client 1: Note 2 is created, with attachment 1
- Client 1: sync
- Client 2: sync
- Client 1: Resource 1 is copied to note 1
- Client 1: Note 2 is deleted
- Client 1: sync, but sync process is cancelled or stopped, and only note deletion is synced
- Client 2: sync, and delete note 2, but doesn't update note 1
- Client 2: Since it didn't get the changes to note 1, it now sees resource 1 as being orphaned, and delete it a few days later
That seems convoluted though, so it's strange that it could happen often.