How do I upgrade ROM with TWRP?

I have nexus 7 running android 4.2.1 and TWRP boot loader. The OTA upgrade doesn't work (presumably because of TWRP). Can someone explain to me how I am supposed to upgrade the Nexus 7 to 4.2.2 maintaining TWRP and root?

Sent from my Nexus 7 using Tapatalk HD

I'm a bit new to the unlocked/rooted scene and run cm10.1, but have you tried unrooting?

Sent from my Nexus 7 using Android Central Forums

Check out the stickies in ROMs rooting and hacks. If you still need help make a thread in there and I'll help you

** these are just words **

I'm having a similar issue. My AT&T one X (rooted, unloced, S-Off) keeps downloading the OTA Update. It tries to install it then boots into TWRP recovery. Install fails from there. Not sure what to do next. I delete the file and it downloads again. I think it's looking for stock recovery to install but I'm not sure how to do that or if I should. Any advice would be appreciated.