I have explained this before. https://support.mozilla.org/en-US/questions/1379670 If you are doing the same thing... You keep making a 'Copy' and putting it in another folder. Gmail does not have 'copies', there is only the original one email and gmail applies 'labels' which are like tags. When you create a 'copy' in Thunderbird, this means gmail applies a 'label' to email on server - it does not make a real copy. Then you choose to delete the original from Inbox. That email gets put into server 'Trash' and then gmail deletes it from the 'All Mail' folder. Gmail does not care how many 'labels' you apply to an email so they can get displayed in various locations - if you delete that email by putting it in the TRash, then all labels are removed and the email is gone. Stop making a 'Copy'. Instead 'Move' the original email from 'Inbox' and put it in the folder you want to store it in. The only other alternative is to delete just the label. To achive that you have to delete bypassing the server Trash by pressing down on 'Shift' key on keyboard whilst you press on the 'Delete' key on keyboard. This is slightly more complicated - hence why I'm advising you to Move the email to other folder.