Agree with the advice about calling again. You just need to find someone sensible at BA who will understand and fix the problem.
IMHO the approach you should take is to get the agent to understand that the flight itself does not need touching, it is the commercial ‘wrapper’ around the ticket that needs swopping from one to the other. Just needs someone empowered to do so IMHO. Sure there is likely to be an admin fee, which personally I would gladly pay to fix the problem, given the value of these vouchers.
PS Explaining this point you made earlier to the agent may help: Barclays Cabin Upgrade Vouchers can only be used for flights starting in the UK, whereas my Companion Voucher could be used for the return flight.