Either the emails are being deleted on the server due to a server setting/filter etc. Or being moved to another email address, hence deleted off server. They may have been downloaded to a pop account used by a phone. Do you access these emails via another computer/phone that could be using pop? Assuming this is set up as an imap account in Thunderbird. Check settings: * Right click on problem imap account in Folder Pane and select 'Settings' * Select 'Server Settings' When I delete a message: * select 'Move it to this folder' and select 'Trash on imap mail account name' * Select : 'Junk settings' * Select 'Move new junk message to' * select 'Other' and select 'Spam on imap mail account name' * Select: Synchronisation & storage' Message Synchronising * Select 'Keep messages in all folders for this account on this computer' Disc Space: * Select : 'Synchronise all messages locally regardless of age' * select: 'Don't delete any messages' * Click on OK. Restart Thunderbird.