As far as I can tell, the backup in iTunes was not backing up mail messages that were on the iPhone or any messages sent from the iPhone. If the only place you had the messages was the iPhone or iPad, you may have lost them. The Info tab in iTunes under Sync Mail Accounts notes that it does not sync the messages. So going back to Time Machine on your desktop won't help because the messages aren't there. At least I can't find them in any of the backups.
Many of us do not have a choice about using POP accounts (Comcast doesn't offer that as an email option). There are pros and cons to POP and IMAP. While I lost the messages on my iPhone, I have it set to not delete from the mail server. Only my desktop does that.
As a longtime Apple user, I am surprised that the mail messages were not backed up as part of the upgrade backup or any recent backup. I thought such a backup had happened in the past. I was very surprised to lose those messages.