Yes it will. Core Updates replace IPFire packages with updated ones so editing those packages risks update replacing them.
The simplest is to create a directory for your scripts and place that script in there. You can then add that directory to
/var/ipfire/backup/include.user
This will then add the contents of that directory to any backup that is carried out on IPFire so your script will also be saved.
There is no Power off on the RPi. You can do a shutdown command and it will stop Linux running but the power will stay on. The only way to turn off the power is to pull out the power plug.
If you run the shutdown command you will need to watch on the serial console one time to note how long it takes so that in future you know when the shutdown command is likely to have completed.