Are you using a POP or IMAP mail account?

If POP: Check you account settings. Tools > Account Settings > Server Settings for pop mail account or Right click on mail account name in folder pane and select 'Settings' then Server Settings for pop mail account.

Select: 'leave messages on server' Do not select either of these: 'For at most xx days' 'Until I delete them'

Click on 'Disc space' Select; Don't delete any messages' Select: 'Always keep starred messages'

click on OK to save and close Account Settings.

If IMAP: You see a remote view of folders on the server. So the folders in Thunderbird and the folders you see via webmail using a browser are one in the same. When you delete in Thunderbird or via webmail you are deleting off the server.

Did this info help?

It is helpful,but my server is IMAP From what you said I cannot delete from Thunderbird because that will delete from my server and I have no other option. Is that correct?

Yes, the folder in Thunderbird constantly synchs with server to update the server and vice versa. IMAP accounts all work this way, so that no matter how you view your emails on the server whether by any email client, webmail - you see the same results.