Flagging the emails will not prevent them from being deleted after a period of time.
I have Comcast email. Go to Settings>Mail, contacts, calendars>Comcast account>Advanced>Delete from server>Never. In the mail settings you can also set more messages to show in the account in Settings>Mail, contacts, calendars>Mail>Show and you can select it to show up to 1000 recent messages. Chances are that the email just isn't showing in the list now because she may have it set to only show 50 messages.
Comcast has their own mail app - Xfinity Connect. I use the app as well. You can actually create new folders on the sever using a web browser on your computer and the folders will sync to the Xfinity app. You can create a folder in which you can save messages and that might prove to be helpful.