Hmm, I'm not sure since I updated first, then unlocked the bootloader then rooted. But even if you do lose root, you can re-root no problem since your bootloader is unlocked already.
If you have CWM installed, you can't OTA, you have to go to stock recovery first, then OTA then go back to CWM
I accepted the update and now have Jelly Bean 4.1.1. I didn't lose any apps or data and then rooted the device again. Thanks to everyone for the advice.