Are you using a POP or IMAP mail account? If Imap, you see a remote view of the server and many servers auto empty the 'Deleted' or 'Trash' folder on a periodic basis to recover space on the server and you have no control over this. If the email is in the Trash/Deleted folder then you have selected to delete it because it is unwanted. The server assumes trash is trash and not 'I've read it and want to keep it for a while just in case'. You should not be storing wanted good emails in the Trash folder for very obvious reasons. Most people realise within a short period of time if they have deleted an email in error and can move it back to a more suitable folder. '''Check Account Settings in Thunderbird.''' Right click on mail account name in Folder Pane and select 'Settings' Select 'Server Settings' for the email account. Bottom right under 'Message storage' Uncheck: 'Empty deleted folder on Exit' Select: 'Disc Space' for the mail account Note if you select to delete emails in this section, it will delete off Thunderbird AND the server regardless of whether Pop or IMAP. Select: 'Don't delete any messages' Do this for all mail accounts. click on 'OK'