Properly update a rooted Nexus 5X with stock Android 7.0 to October Security update
From XDA Developer's [GUIDE] Unlock/Root/Flash for Nexus 5X, I went away and:


Downloaded the OTA zip file
Installed the Android SDK tools,
connected my device and rebooted it into TWRP
Then went to Advanced -> ADB Sideload
Then from the command prompt, typed "adb sideload /path/to/OTA/zip/file" and hit enter
It took a few minutes to 100%, then I rebooted my phone and all is well and updated now.
Re-rooted my phone using NRT.