I haven’t tried this feature yet. I can maybe test it later. But in the meantime:
If you open that “Excluded folders” settings on your computer, did those folders get checked on your computer too? Or are they not showing up in that list anymore? (actually disappeared?)
Can you please confirm that you are talking about “Selective sync” and “Exluded folders → Manage”. Because in your post you said “manage synced folders”. Let’s just make sure we’re talking about the same thing. I think we are, because you replied to jwl. Just making 100% sure.
Can you see those missing folders if you go to “Deleted files” in the Sync settings? Maybe they were deleted, and not just selectively unsynced.
You also have the sync log to see if you can spot any problems that happened.