I had to open Logos offline today, due to the server problems. During that time I made a note including a manually linked scripture reference. The link worked directly after it was made, but as soon as I went on to something else, the linking disappeared. I tried several times.
Fortunately, I noticed it directly, and fortunately the servers had just started working again, so I could restart, redo the link once again, and make sure to sync, after which it did stick, so I wasn't too badly affected -- but if I'd been in Africa doing hundreds of notes in offline mode, I would have been very unhappy when I found out...