They've done it a little differently on different ships but overall, they've refunded the list price of the excursion, less any latitudes discount, then charged $50 to recoup the FAS discount. So the refund you got + the $50 charges should net what you actually paid.
Then charged for the new excursion, less any latitudes discount ( you have to ask for that, it's not automatic). The $50 FAS discount will come off overnight, after you've taken the excursion.