I just flashed the OTA to my Nexus 7 2012 by sideload using TWRP and you will lose root, but it is an easy process to restore with Mark Skippen's or Wugfresh's toolkits.
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After owning the original Nexus since July 2012, I still feel like a newbie, so I always ask for help. Hope you don't mind
Will the applications be lost also ?
If so can I recover these applications from my nandroid back up using Wugfresh tool kit ?
Can you give me step by step guides ?
Is the OTA you referred to this file ?13088e35942c77e4752aa1fdf51d54472509b941.signed-nakasi-KRT16O-from-JWR66Y.13088e35.zip
Since the file name is too long, can I rename it such as Update.zip ?
Where do I put this file before sideloading in TWRP ?
How do I side load ? using TWRP ?
Mine is Nexus 2012 unlocked and rooted with 4.3 version