After 30 days of inactivity, the mail is deleted. After 90 days of inactivity, the account is deleted. This might be what happened, but she should be able to re-activate the account. Messenger usually isn't affected, I think the sign-in name just becomes a basic Passport account or something.
Also try accessing the account from Messenger's main UI, either thru the inbox button or right-click a budy and send email. Also, a good tip to automatically keep your account active is to turn on MSN Today, since it has to access your Hotmail account and thus keeps it active. Then click to view the Hotmail tab after it finishes loading, and that will be the default tab that always comes up at logon.