I had this same problem myself. I just rooted the phone, and did my nandroid restore of Tranquility and used the toolbox to flash the boot logo and animation back to stock. Then after this, I SBF'd and sent it in.
Maybe there is an easier way to do this, but this didn't take that long for me. Not sure if the Tranquility Toolbox will work on just a rooted phone, maybe somebody here knows.