If this is an imap mail account, some servers auto delete messages that are in the 'Deleted/Trash' folder. Is this a pop or imap mail account? What is the bit after the @ eg: is it gmail, yahoo, comcast etc ? '''Check your Thunderbird settings for those folders.''' Right click on mail account in Folder Pane and select 'Settings' Select 'Server Settings' bottom right 'Message Storage' Uncheck 'Empty Deleted folder on exit' Select 'Junk Settings' Bottom right 'Destination and Retention' uncheck 'Automatically delete junk mail older than XX days' click on 'OK'