A few years ago there was a case where conflicting case in the shelf/collection names could break syncing:
https://www.mobileread.com/forums/sh...29&postcount=6
https://www.mobileread.com/forums/sh...07#post4174307
Interestingly, purging my collections resolved the sync issue I was having. Only 10 cats, but a few had 100+ books. It's possible that there was some issue similar to the case-sensitivity though.
I'm going to nuke fiction and freebies, and look into splitting others to see if it helps.