I booked a BA-operated TATL issued on AA stock on March 2 with Omega.
Due to a schedule change, I called AA and after explaining the situation, they checked to confirm the ticket was paid for.
They (reluctantly) took control of the ticket, made the necessary changes and re-issued it.
It sounds like you already have an e-ticket issued. I could be wrong, but I thought an e-ticket only gets issued after the agency has paid.