What is your antivirus? Check your antivirus-quarantine. Have you set it to NOT scan your profile? If not DO IT.

As every folder is a single file there could be some mail-attachment that is, by mistake or not, to be suspicious with the result that the whole folder is removed.

Most antivirus scan mail when it's downloading in cache to fetch any infected mail.

An update of TB should not have that effect as it updates files in C:/programs and not in your personal profile-directory.

Thanks for the reply Gnospen, I did check w/ my antivirus quarantine files which were empty.

With TB not running: enter in explorer %appdata%\Thunderbird\profiles There is a directory "some-numbers and letters".default or equal open that. Find and open directory MAIL then LOCAL FOLDERS. Look if you can find your missing folders here, thats files without an extension. Either direct under Local folders or under some subdirectory "foldername".sbd If you find them DO NOTHING.

Make a safety-copy of your profile or at least of Local Folders.

Start Thunderbird and install an add-on Recover deleted messages by Kaosmos Use this to undelete any messages (Works only if you DIDN'T compact)

If you don't find the folders.... hopefully you have regularly backed up your mail ?????