It looks like Thunderbird silently deleted some important folders (I wondered why some messages remained in the inbox). It looks like the directories and mails still are there, e.g. in Data\profile\Mail\local\<containing-folder>.sbd\<folder>.
How can I restore the folder in Thunderbird?
It looks like there is not just the <containing-folder>.sbd directory, but also a <containing-folder> file. After having restored that from a backup, I could access the subfolders again. If the <containing-folder> did not contain important information, but the subfolders do, one also can reactivate the subfolders by creating an empty <containing-folder> file.
My situation was that the mail server was wiped and I only had Thunderbird local copies. The only way I was able to make Thunderbird see those folders was to copy the IMAP mailboxes to the Local Account, see the images below. Make sure Thunderbird is shutdown, also there was some corruption but it was better then nothing, I don't think the .msf files are needed as they are re-generated.
Assuming that you are connected to an IMAP server and running on Windows 7, the data is stored in:
C:\Users\USER\AppData\Roaming\Thunderbird\Profiles\yg4g294c.default\ImapMail
Where "USER" is your user name and "yg4g294c" will be different on your system.
In that folder, you will find a bunch of stuff including sub-folders for each server you connect to. An in there are a sub folder for the top level of the mail server and in there are files that contain the actual mail.
It should kind of make sense when you look at it.
If you are using POP3 rather than IMAP, I think you should see similar things though with a slightly different layout under a POPMail folder - though I'm a little rusty on POP3 mail in Thunderbird as I haven't used it for a very long time.
Restoring though is going to be trickier if you are using POP3. Using IMAP is easy, delete the profile and start again. Though that does loose your filters, saved searches and so on so export what you want before deleting. With IMAP, everything is kept on the server and Thunderbird just keeps a local copy if you ask it to.
Let me know if you are using POP3 and find a file for the folder you want to restore and I'll try to remember how to restore it (if it is possible).
