In this situation you are best off confirming removal of one FFP and insertion of anoer with an agent at check-in or in the lounge before flying, not just by using a self check-in machine. It is worth checking they have updated the FQTV (mileage accrual) field and not one of the other frequent flier fields in the airline's system such as FQTS. Input of FFP numbers into airline systems at self check-in machines or online do not always follow through to the correct field if an entry already exists.
As others have posted, in thiis situation hipefully A3 will now credit the miles. I would fax/email A3 the BP showing your A3 FFP number and also a print of your mileage statement showing both the original credit to and the reversal of the credit by UA.