Default [Q] /system/app/books.apk unexpected contents. But no such apk exist!

My Nexus 7 LTE is rooted with stock ROM. I am trying to upgrade to 4.4.2 and it failed because of the error message:

/system/app/books.apk unexpected contents. Installation aborted.

However, searching the folder using ES Explorer, I don't even see this books.apk

My questions are:
1. How is it possible the upgrade fail for an apk that didn't even exist?

2. If all else fail, what can I do to upgrade to 4.4.2 via OTA?
Galaxy Note 3 T-Mobile
Stock ROM - rooted
Official Jelly Bean 4.3

Note 10.1 (2014)
Stock ROM - Not rooted since KNOX tripping
Official KitKat 4.4.2

Nexus 5
Nexus 7 (2013)
Galaxy Note 8.0
Nexus 7 (2012)
AT&T Galaxy Note
AT&T Galaxy S4 Active