So how do you do an update when you're rooted? I've received an OTA update since rooting and every time I hit to update it reboots into the twrp-recovery screen where I just end up restarting back into the system because I'm not quite sure where it downloads to. Then I see the update notification shortly after again.
Here's the easy method I employ when applying an OTA on a rooted stock ROM:
- Download the Android SDK Toolkit (with adb)
- Download the factory image for your Nexus 7 and save it to the same directory (good to have anyway)
- Download the OTA zip file from somewhere
- Rename it to update.zip and save it to the root of your internal storage
- Flash stock recovery back onto your device using "adb flash recovery recovery.img"
- Now, within stock recovery, select the "Apply update" option.
- Your device will update successfully.
After that is done, you can flash your custom recovery and root back onto the device with no problems. The only thing stopping the OTA from working in your case is that you're running a custom recovery.