I've looked at what I've done and what changes I did mean, and I think theres no rescue. I'll have to get the department to resend everything if they can. But some other stuff is defo lost for good which is a fucking pita.
Error was in my not realising that the mail server didn't support the remote creation of folders for sub storage. So those folders only existed in thunderbird in the inbox, but not in local storage. So when I synced with the folders on the server, those synced folders superceded the ones I'd already made offline, but which thunderbird thinks are connected to folders on the server which don't actually exist. So the proper syncing deletes them because they're not actually on the server (inbox subfolders instead of local subfolders). And the messages in them aren't on the server either because the remote folder creation doesn't work.
I've run an undelete scan and the files which would have represented those now missing folders haven't appeared. So because of a culmination of ineptitudes, they're gone with no hope of getting them back.