Upgrade Android 4.3.1 from a Rooted 4.3

Google unexpectedly released an Android 4.3.1 when everyone is expecting the release of Kit Kat 4.4  is just around the corner.
This OTA seems to be pushing only for the Nexus 7 LTE model first.

Method 1:

1. Go into SuperSu settings to enable survival mode.
2. Download the OTA directly on your Nexus as you would without root and restart to install.
3. It will be installed by TWRP, root will be kept, but TWRP will be gone.
4. Reflash TWRP in Fastboot.

Method 2:

Buy the SuperSU Pro and enabled the survival mode.
OTA, installation with TWRP and rebooting ok.
Then reinstalled TWRP with Goo Manager.

Method 3:

If you update in this exact order, you will keep both root and TWRP. Note it needs to be SuperSU 1.55 (not the latest)

• download OTA zip, place on virtual sdcard
• download SuperSU v1.55, place on virtual sdcard
• boot into TWRP
• install OTA zip then immediately (prior to reboot) install SuperSU zip

Note:

To get the OTA to appear again you will need to go to Settings, Apps, clear data / cache for "Google Services Framework".