There’s something wrong with the count of needed files then. That is separate from the actual list of needed files, as evident from the discrepancy you see.
I had a similar experience when adding “.DS_Store” to my .stignore (it’s a Mac thing - because the colleague I’m syncing with has a Mac). When I reorganised our shared directory I noticed that some directories I had moved later reappeared in their old places, apparently empty, and the GUI was saying “Out of sync” with these zombie directories listed as the files that were needing to be sync’d.
Manually deleting the .DS_Store files fixed the problem. For now, I’ve removed my .stignore.