Like most of you, I too lost root on my Asus Transformer Prime when I updated to Jelly Bean. I just didn't get around to doing anything about recovering it until now. I tried installing TWRP and it failed. I had sent in my TF201 for repair and I think they locked the bootloader because I know I had unlocked it. That tells me either there is an error in the TWRP installer OR the bootloader was in fact locked. Thinking the latter was the more likely case, I decided to tried to unlock it. I had read that the Asus unlocker no longer worked on a TF201 on JB 4.1.1 but I figured I would try anyway.
*** If you follow these steps, it's your responsibility. Standard disclaimers apply. You know the drill. ***
I grabbed the unlocker here: http://forum.xda-developers.com/showthread.php?t=1510737 and downloaded the one from the Asus site. Copied it to my SD card and ran it. I agreed to the big scary EULA and proceeded. It took a while but I got a network error message. Undaunted, I tried again. Hey, repeated actions do sometimes have different results. This time, teh app noted I didn't have a Google account installed and did I want to continue anyway. Damn straight I did ... and it failed saying something like "too Busy, try again later." I had reset my TF201 to factory, so I added my Google account to my TF201 and tried a third time. This time the app asked me to login to confirm my account. I did and it unlocked. w00t!
I wonder if those who are on JB but didn't unlock while on the ICS bootloader are screwed now while those of us who had unlocked while on the ICS boot loader but for whatever reason have a locked bootloader (I sent mine in for repair) are fine. Seems to be the case.
At this point, If I just boot up, I see the "The Device is Unlocked" message. If I boot into recovery (press VOL down + Power), I don't see it.
Next, I followed the steps here (http://forum.xda-developers.com/showpost.php?p=26595675&postcount=2) to install TWRP. Success!
Then I grabbed the Superuser binary http://androidsu.com/superuser/ and dropped it onto the SD card. Booted into recovery (TWRP) this time and installed SU. Sweetness.