POP Collector should only mark a message as downloaded and sent once it has actually been sent (i.e. SMTP conversation returned an OK response when sending). I will check to see if I can find a problem here.
In the meantime, to delete the tracking info, you can simply delete the MessageLog.mdb database. This will automatically be recreated when PC is started, and will force all messages to be redownloaded and forwarded. This does however apply to all accounts, there is no easy way to only apply it to one account.