If you sychronise your iPad with your desktop computer regularly what is on one should be the same as what is on the other.
What gets completely deleted depends what folders you keep emails in. If you keep emails in 'local' folders on your machines, the originals will not be affected on the server. You need to delete them on the server. This is done by putting them in the trash of the server, not your local trash.
I read my emails on my ipad and on my desk computer. If I delete emails on the ipad then go to the desk top computer the emails are still there although they have vanished from the ipad. My server is yahoo. I've googled the query but there is no answer. Has anyone had this problem and solved it?