We've been recommending people using Thunderbird for years. Thunderbird is just as good as paid email programs if it's not better. As it's getting very popular, there are some works our customers might need us to do.
A customer rang me today and she lost some folders in Thunderbird. Eventually I found the folders she needed actually just sitting in the Trash Bin, so no big deal. But during investigation, there are chances you can recover folders after you emptied the Trash Bin, as long as you haven't perform the "Compact" function.
The deleted folder will be inside the profile folder, something like jj8sj53o.default, then depends on your settings, it's under Mail/ImapMail, and the Trash Bin in gmail should be like this
For example a test folder in Trash Bin, you can find two files under Trash.sbh folder, and the files related the test folder are two: "test" and "test.msf". All the emails inside test folder are stored in those two files.
So to recover your thunderbird folder, you need a recovery program to recover those two files first and then move them to the original folder.
The location for Thunderbird profiles:
C:\Users\[YOUR USER NAME]\AppData\Roaming\Thunderbird\Profiles\xxxxxxxx.default\