I have this same, exact problem. Typically, I use mobile to rate and cull, so I don't lose an insurmountable amount of work. I haven't had the problem in awhile, and the opportunity arose today, so I did some (nearly) full edits on mobile. Cut to me on my desktop seeing that only 13/25 images I had flagged are actually flagged, and those which the rating is not appearing the edits aren't there, either.
It seems like the only solution is to delete all sync data and lose everything that hasn't come over? Unacceptable.