Accumulating messages in Inbox is a bad idea. The file grows over time and every time you receive a message the entire Inbox file is scanned by anti-virus software while Thunderbird needs to wait to write to the file. Anti-virus is the most likely to have cause Inbox file corruption which can cause data loss. These are some generic suggestions to avoid problems with anti-virus software. Create an exception in your anti-virus software for the Thunderbird profile folder, so that the anti-virus real-time scanner will not scan it. https://support.mozilla.org/en-US/kb/profiles-where-thunderbird-stores-user-data#w_how-to-find-your-profile Don't let your anti-virus software scan incoming and outgoing messages. Don't let your anti-virus software scan attachments. Don't let your anti-virus software intercept your secure connection to the server. Remove any add-ons your anti-virus software may have installed in Thunderbird. Keep it working. http://kb.mozillazine.org/Keep_it_working_-_Thunderbird And last but not least, backup your Thunderbird profile on a regular basis. https://support.mozilla.org/kb/profiles-where-thunderbird-stores-user-data#w_backing-up-a-profile If you do have a backup created prior to the incident that would probably your best bet to restore the lost messages. To avoid accumulation messages in Inbox in the future take a look at the Archive feature. https://support.mozilla.org/kb/archived-messages