Updating OTA after changing /etc/system files
As far as I know, you first need to unlock bootloader to root a nexus device (I'm not a nexus user). 

Now, in order to update your OTA, it is mandatory to lock the bootloader and then perform the update. 
I'm a HTC user, and I faced the same issue. What I did was flashed the stock recovery, locked the bootloader and performed the update. Everything went smooth. 

I'm sure nexus follows the same path.