How to perform FileVault authenticated restart when updating OSX from AppStore?
It sounds like you want the next restart, whenever it might occur, to skip FileVault authorization. You can use the -delayminutes option with a value of -1 for this.
From the fdesetup man page:

authrestart [-inputplist] [-delayminutes number_of_minutes_to_delay] [-verbose]

If FileVault is enabled on the current volume, it restarts the system, bypassing the initial unlock.   The optional -delayminutes option can be used to delay the restart command for a set number of minutes.  A value of 0 represents 'immediately', and a value of -1 represents 'never'.  The command may not work on all systems.

Try running the following command before the system update:
sudo fdesetup authrestart -delayminutes -1