Whether mails get marked read online when downloaded by POP3 is a feature of the mail server. Some servers will mark them read - because they were downloaded once, the server assumes you saw them. Outlook doesn't care about the read/unread status online, it tracks mesages on its own. It knows the last downloaded message and has its own read/unread state.
to redownload mail you need to make a new account in outlook - you could probably delete the mailbox manager hidden message using MFCMAPI. Note that you will redownload everything - you can't tell it to only re-download some.