Gamestop has some weird policies regarding money. Its not a pre-order case... but this happened to my brother.
He went and bought an used copy of Yakuza for PS2. They gave him the game in an envelope without box or manual, so I told him to return the game.

The store clerk decided to refund him the money only because: 1) He returned the game under 7 days and 2) He didn't open the 'sealed' GameStop envelope. If he had taken more than seven days or opened the envelope, they would have refused to return the money and would have given him store credit.

I've never pre-ordered on GameStop... but if thats the policies regarding used games... it wouldn't surprise me if pre-order money would be handled the same way, through store credit.