Hi there rosefromsaintjohn,
Managing email is definitely an important task, and we see you're running into a few issues on your iPad. We'd like to learn more about what's happening to see how we can assist.
It sounds like this is happening with an @iCloud.com mail account. Is that correct? If you use any other mail accounts on your iPad, have you noticed similar behavior with those accounts?
Do you use the same account on any other devices? Are you able to permanently delete an email from the other device?
When you say you can't see emails that you kept in your Inbox, what exactly is happening there? Are you finding that mail doesn't load when you open the app, or something else?
Also, what happened exactly on the iCloud website? As a test, when you delete an email directly from the iCloud website and empty the Trash there, does it still return to your Inbox?
Let us know how it goes!
Best wishes.