The answer is simple: you would get the pro-rata amount back of the full (‘book price’) Advance Payment.
So, using your example, if BMW sold you a 3 Series for £0 AP, but it was in the price guide at £1,999; you would get a pro-rata refund based on £1,999. Crafty, eh?
Your Advance Payment goes to the dealership, but it does not go to Motability. Instead, it fills a gap in the dealership’s invoice. For example, the BMW I used above: let’s say it’s worth £24,999 as a Motability sale to the dealer; the dealership would get £23,000 from Motability and £1,999 from you = the invoice amount expected.