I think what might be contributing to the lingering BAEC number is that it's originally entered in the Amadeus PNR, and then, when the check-in record is created in PRS a day or two before the flight, it gets copied over to that record. So it's now in two separate systems: the PNR, and PRS. I would imagine that my colleagues are removing it from PRS but not the PNR (or vice versa) and so one or the other of them is still tracking.
If you get the check-in agt to remove it from both, you'll have to have it added again for your return, so you can still retain the seating selection you're entitled to (before it's removed by anyone/anything looking for bookings with seats that shouldn't have them).