Three jaychant posts in my thread is exactly three posts too many.
It makes more sense as:
Old top speed * (New acceleration increment / Old acceleration increment)
Assuming Old acceleration increment is the ship's original value, this method means that ships with a high (original) acceleration increment are less heavily affected with regard to top speed than ships with a lesser acceleration increment (because the above quotient will be closer to 1 for them).
TfB probably did this because they thought the (original) acceleration increment shows how "snappy" the ship is more than its (original) top speed, and they wanted to reward those snappy ships.
By the way, this isn't an "algorithm" really, it's just an arithmetic formula.