I second this, as disheartening as it is you're on the precipice of joining the few true MMO's that are available on the App Store. Apple's QA and app review process is a notorious headache for the most seasoned developers, but I guess you guys knew that. Take it as a learning curve and as they say: "Third time lucky!"
I'd place a safe bet that the guys will be using some sort of versioning method that will allow them to rollback the game back to before the changes were made, should the case arise.
Don't take it to heart guys, you've done so much in preparation for this moment. Don't let it slow you down.