Thunderbird: Mails are not visible in inbox or appear twice?

"Try the following (backup the files first, please)

Close thunderbird
Go to the profile directory, and delete the index file (.msf) for the folder in question
restart thunderbird.

Has worked for me a few times. BTW, the issue generally occurs when using IMAP and interrupting download/sync of folders - esp when a large number of messages are being synced. Is this the case here too ?"