Thunderbird does not delete messages from the POP server
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Go to Options -> Advanced -> Config Editor.
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Find the Name
mail . pop3 . deleteFromServerOnMove -
Set it to True.
True: Delete the copy of the message on the POP3 server if you move or delete the message.
False(default): Only delete the copy of the message on the POP3 server if you delete the message.
That's it, restart Thunderbird. You need to press 'Get Mail' everytime you want to sync with the email server, in order for you to make sure messages in the application is in sync with the email server.
The following should be emphasized to realize the sync with the server. You will not see your server message disappear upon the initial Get Mail download (new messages downloaded). After you process your Inbox in Thunderbird by deleting/moving a new message, then do another Get Mail which will delete the new messages previously downloaded on the server (put in sync).
Note: If you have older messages in your Thunderbird Inbox, they will not be deleted from Server. Delete them manually from server. From then on, any new messages you download, then process (delete/move), and then do the sync by doing Get Mail again WILL be deleted.
Did you just delete it in Thunderbird, or do you already empty your trash can?
In my Thunderbird, the Mails are deleted from the GMX server as soon as the mail is deleted from the trash, not while it is still in the trash can.