you dont need to worry about it. all they care about at this point is that they get a phone back. there is absolutely no way they will find out the phone is rooted, and even if someone did, they wouldnt take the time to trace it back to you, and give you some sort of hard time about it.
of course, if you are paranoid, it wouldnt hurt to sbf, but it is completely unnecessary. it is verizon's job to determine whether a phone should be covered by the warranty. once they have determined it has been affected by a manufacturer defect, and thus replaced the phone, they cannot then turn around and take any recourse against you. it is now their fault they replaced a phone that is technically no longer covered by the warranty.
so, to make a short story long, you have absolutely nothing to worry about. I work for Verizon (behind the scenes) and i am well aware of the policies and procedures, so you can trust what i'm saying.
what's funny, is that i have a friend (fellow employee) who had some problems with his first X, and in the return box, he put his old moto droid (and sold the x on ebay), and they never even noticed that. and before that, he got a replacement moto droid, and sent back an EnV3. so trust me, they do not look very closely at the phones that are being returned, just that they ARE being returned.
DISCLAIMER: I absolutely cannot recommend you try to send back any other phone than the one that is being replaced. My friend's experience was likely a fluke. I am not responsible for the $569 charge on your bill when you send back your old LG Dare instead of your Droid X.