I thought I notice this a while ago.. but I think I finally have proof..
Scenario:
I deleted all of my documents by right clicking on them and choosing delete
Observation:
I thought I would check my database and was surprised to see orphan records, so I presumed it hadnt finished syncing, I clicked on the sync wheel and it synced and said "all items up-to-date"

Looking at the file tho there were records left..
I then deleted my documents folder in ~\Logos4\Documents\qt1zgzl5.1t3
so I started with no documents (or there should not have been any) it recreated the files, then when I restarted Logos and it spent a while syncing, which seemed funny for no documents.
I have also run the "sync now`" command, at end Document window shows nothing even after a restart

however when I look at the file... it says there should be 4 notes

Here are the newly repopulated document directory files
3755.Documents.zip
Surely these should not sync if they are to be orphans??