I am not sure I follow this at all. You booked via a travel agent (TA)? With BA miles? As far as I know this is only possible with for MFUs with a very few preferred North American TAs.
The flight has disappeared. Have you got the booking reference? Have you tried entering it into ba.com on MMB? It may be disassociated with your BAEC account for some reason.
On cancelling the flight, normally TA booking means dealing with the travel agent. BA can only alter the booking from T-24 and unless you have a fully flexible ticket that is likely to be too late.
Sorry that this isn't very help, but perhaps you could clarify the facts to help everyone on here help you.