From MozillaZine Knowledge Base
- This article was written for Thunderbird but also applies to the Mozilla Suite (though some menu sequences may differ).
This article describes what to do if some or all of your messages disappear. However, if Thunderbird suddenly ran the new account wizard when you started it, see Recovering a profile that suddenly disappeared.
The first thing to do is to try to figure out what the missing messages have in common. For example, is the problem limited to one specific folder or account or just new messages? Did you lose the messages shortly after changing the configuration? Look for anything unusual or that doesn't look right (besides some of your messages being missing) and then use the following checklists.
- Check to make sure that "View -> Messages" and "View -> Threads" are both set to "All". Set "View -> Folders" to All. Sometimes a Unified view has problems. Set "View -> Sort by" to Unthreaded. Sometimes a conversation view hides messages. 
- Check for incoming messages that might have been sent with an incorrect date. That can make the message hide anywhere among old messages in the list, due to the sorting. Check that the system date for your computer is correct - if it's incorrect, that could cause messages to appear out of sequence.
- Check that the search field in Global Search and the Quick Filter bar is empty.
- It's possible that the ".msf" files (index files) are corrupted. To rebuild the index of a folder, right-click it, select Properties, and choose "Rebuild Folder" from the General Information tab. You can also close Thunderbird and manually delete them from your profile folder; they will be rebuilt when Thunderbird starts.
- Check whether some of the messages in the folder are fragmented or compacting doesn't seem to work. You might also see some of your messages having dates of 1969 (due to a missing a Date: header) or the summary file being rebuilt whenever you open a folder. If this happens your folder is probably corrupt due to not compacting it regularly. Depending upon how corrupt it is it might have just hidden or permanently lost the missing messages. See the second method in Compacting doesn’t seem to work.
- Try running Thunderbird in safe mode (not to be confused with Windows safe mode) to temporarily disable any added extensions or themes.
Global Search specific
- If you can find and read the messages except when you globally search for them, then the search index is probably corrupt. In that case exit Thunderbird, delete the globl-message-db.sqlite file in your profile, run Thunderbird again and let it rebuild the search index. This can take a long while, depending upon how much mail you have. Quick search (Edit -> Find -> Search messages or Ctrl+F) and the Quick Filter bar don't use that file.
It's just doing what you told it to do
- Is Thunderbird working online? Check Files -> Offline -> Work Offline is not checked, and that you can do something that gets a response from a mail server (download a new message, send a message, list subscribed folders in a IMAP account etc.) to prove that your firewall is not an issue.
- Could you have deleted the message? It's easiest to recover them if they are still in your trash folder. If you haven't compacted the folder, see Undelete a message for several ways to recover deleted messages.
- Look in the Junk and Trash folders. Depending on how you have the Junk Mail Controls set up, messages can be sent automatically to the Junk folder or Trash.
- If you have any message filters they might move or copy new messages from the Inbox to other folders. Check your filter definitions in "Tools -> Message Filters" and choose the problematic account from the top drop-down-list. You can check the log file by pressing "Filter Log"; if logging is disabled you may want to enable it to help if the problem recurs.
- If you are using the message aging feature, it will permanently delete messages based upon your settings. Right click on the folder, select Properties, Retention Policies, and verify that it's either set to "Don't delete any messages" or - if it's set to "use my account settings" - that Tools -> Account Settings -> Synchronization & Storage -> Disk Space -> Don't delete any messages" is selected. (If you're using 220.127.116.11 or earlier uncheck Tools -> Account Settings -> Offline & Disk Space -> Disk Space -> "Always delete read messages")
- Did you read any of your messages with a different email client? If so, whichever one checked for new mail first might have deleted the copy of the new message on the POP3 server, preventing the other email client from finding it when it checked for new mail. You can prevent this by setting the equivalent of Tools -> Account Settings -> Server settings -> "Leave messages on server" in both email clients. If you do that, you might also want to check "for at most X days" so that your mailbox doesn't become full. If you're using the same Gmail POP account with multiple email clients you need to enable recent mode in order to let each email client access all of the messages in that account. You can do that by replacing firstname.lastname@example.org with recent:email@example.com as the username in Tools -> Account Settings -> Server Settings.
- Look in your profile folder and see if you have multiple copies of a account directory. For example, if you have a Gmail POP account you should find a pop.gmail.com directory (it's named after the mail server) in the mail directory. If you also find a pop-gmail-1.com directory (or some other numeric suffix) your messages for that account might be spread across multiple account directories due to some error. The only time you should see account directories with numeric suffixes is if you created multiple accounts with the same mail server but different user names.
Use the browse button at Tools -> Account Settings -> Server Settings -> Local Directory to browse to your original account directory (Tools -> Account Settings -> Local Folders -> Local Directory if it's a global inbox) and then press OK. If some of your messages are still missing, import the folders in the other account directory using the ImportExportTools extension. If you're using Firefox to download the extension remember to right click and select "save link as" rather than left clicking, in order to avoid Firefox trying to install the Thunderbird extension.
- If mail disappeared from the message list immediately after you renamed a mail folder or subfolder, try exiting Thunderbird and restarting. If that doesn't work, exit Thunderbird, go to your profile folder and rename the corresponding mail file and delete the panacea.dat file. 
- If the messages are deleted but you haven't compacted the folder yet you can undelete the messages. If you want to try that backup your profile first using something like MozBackup.