If you have backups, this directory contains all of your mail and profiles:
C:\Documents and Settings\kellie\Application Data\Thunderbird\Profiles
(where "kellie" is whatever you log in as)
Before proceeding, save everything in that directory to a backup directory. Somewhere in there is a folder "Mail", and then a folder according to your mail server name, and that's where all the mail is saved. You can try to rebuild individual mailbox indexes by deleting files with a ".msf" extension.
Also, you may want to just reboot first if you haven't. Sometimes T-bird will leave a copy of itself running, which confuses the second copy of it when it goes to read everything.
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