So I went partial-nuke and deleted only one account instead of blowing away all accounts and all local mail/folders. After deleting that account I made sure to delete the re-appearing folder from the server, waited 30 minutes and then recreated that account on the Mac, pointing it to the correct IMAP folder. It's now synchronizing all the folders and their contents.

This should indicate a difference between this account and the other (affected) one that I haven't yet deleted/re-created.