If you get the "back office" route - so no breakdown of the refunded presented on screen - then if BAEC (or rather IAG Loyalty) make a mistake with the calculation you can still get that corrected after the event. The problem in this area relates to Commercial bookings rather than Redemptions, where the Commercial booking rules are quite different to Avios bookings and where you can blindly ask for a refund, only to get very little back.
The bigger complication relate to Commercial bookings where Avios was used to part pay - and depending on the details, the Avios there may not be refunded but will form an indirect aspect to the cash amount, which indeed could mean no refund of the Avios.