In reply to captain paranoia:
You can often choose whether deleting emails on a client device also deletes them on the server as a setting on either client or server.
Depending on how many years she's had the iPad, it may have synced with Hotmail using the old fashioned POP3 protocol which is only really designed for using a single email client to access your mail. By default, it normally deletes mail from the server when the client downloads it. This can be overridden but it still doesn't tend to propagate changes on the client back to the server. It's mostly a one-way system which makes it a pain to use with multiple clients or, as you're discovering, to switch to a new one.
As far as I'm aware, there's no easy way to now get all the changes and deletions she's made on the iPad to transfer to the server.
Moving forward, you should probably make sure that both iPad and iPhone use the more modern IMAP protocol to communicate with the server. That's designed to be used with multiple clients so changes like deletions or read messages are propagated both ways between clients and server.
Microsoft will have the details you need on their help site.