The only way that I know for sure to work is to recreate your folder structure and to import each folder seperately, but you mentioned that that's a path you want to avoid.

You might try this. As you've managed to store everything on an imap server and have TB (The Bat!) access that, make sure you've cached everything, (TB recreates the folder stucture for its local cache)
create a new pop3 account, but don't start to download any mail into it as the rest of the procedure would cause that to get lost.
Close TB (without any compressing on exit)
copy the folders and their contents from your imap account to your pop3 account, copy just the subdirectories and their contents, don't copy the files in your account directory as those contain the account properties and all you would achieve is to create a second imap account.
After doing this you can start TB again, your pop3 account won't show any additional folders, but selecting your pop3 account in the account tree pane and pressing Ctrl-Shift-Alt-L should cause your folder structure to emerge and with any luck also the messages that are supposed to be there.
Note that I've never tried this, as I never played with either Thunderbird or IMAP.