This is the problem with prepayments. If quantity or prices change it doesn't work well.
1 - receive and invoice the 98, this will leave a balance on the prepayment for a quantity of 2.
2 - receive and invoice the other 2, this will use the balance of the prepayment
3 - create a credit memo for the quantity of 2, this will remove two from inventory and put a credit on the vendor account so you know the vendor owes you money back.
NOTE: I would try to your the same vendor invoice number for both 1 and 2 something like 12345 and 12345-2. And for your credit memo use vendor invoice number 12345-CR. This will help in the future to remind you of what happened. (substitute 12345 with you vendor's invoice number or POnumber)
This won't work for every iteration of what happens with a prepayment but it will handle this situation.
