In the game you described, the player was down by contact.
(I'm assuming your HL didn't signal TD.)
In a normal game situation, A has the choice of replaying the down or the result of the play. The whistle was blown while the ball was loose so result would be the end of the run. I don't have my book in front of me and it's been a long time since I've actually seen an IW, but I think that's right. If not, the board will correct me.
So, replay the down from the 3 or next down from the 1/2 yardline.
Then the HL has to buy beer for the rest of the season. There should never, ever, ever be an IW. (Yes, I had one when I was a rookie - cost me a couple of game checks in beer.)