It sounds like your mail files were corrupted. When attempting to rebuild the index file of a troubled folder Thunderbird is trying to repair the damage already done. Depending on the corruption this may erase messages from the affected folder which cannot be recovered anymore. In that case you'd need to restore them from a recent backup done prior to the corruption. Corruption is often caused by anti-virus software messing with Thunderbird mail files. It is therefore recommended to create an exception for the Thunderbird profile folder, so that the real-time scanner won't attempt to scan the profile with your mail. For more information on the profile location see http://kb.mozillazine.org/Profile_folder_-_Thunderbird Also see http://kb.mozillazine.org/Keep_it_working_-_Thunderbird Make sure to create backups of your profile folder on a regular basis. https://support.mozilla.org/kb/profiles-tb#w_backing-up-a-profile