Im in similar circumstances , I placed my order on 13th September but the dealer changed it to the lower AP when the price dropped on the first of October.
This process does not make any alteration to your order with Skoda. It purely changes the order date on the motability system.
When you go into your account on MB your application approval date will have changed from your original order date to the date you updated for the lower AP.
Your original order on the MB system at the higher AP no longer exists.
I’ve had a hectic year with Enyaq orders. I ordered a 60 in April and cancelled when it arrived in UK and reordered a coupe. Cancelled and ordered the Sportline plus SUV when that came on. Then had the dealer adjust the order for the lower AP. So technically I’m on my 4th order.
Your previous order for a higher AP no longer exists as when your order changes on the MB system the PIN number you are issued will only work for that order.