The old messages would have to be sitting on the mail server to re-sync after the mail account is set-up on the iPad. Sounds like typical POP3/SMTP account behavior to me, with a keep mail on server setting on the server side.
If it were an IMAP account, any change on the home PC or IPad side would then be updated to the server and therefore each other.
If the former, a similar thing will occur again the next time a new iPad, iPhone, etc. is set-up with that mail account. I would be checking the server-side settings for a solution. Probably the best place to clear the unwanted emails as well.