The upgrade to fiber from an analog phone line does not usually create a problem for the alarm system provided it is installed properly. The bigest issue is the phone line normally runs through the alarm system before the house phones. If the installer of the fiber box runs the new line from the fiber box directly to the house phones the alarm system will be bypased and it will no longer communicate.
One of the biggest differences between Fiber and analog is where the phone line gets its power. The older analog system was powered from the central office and in a power fail the line on an older phone it would still work. For the new fiber system the fiber box needs a backup battery in order to work in a power fail. Make sure they install this component as per their documentation or your alarm system will not communicate during a power fail.
Home phone battery backup system