What you're describing is quite common. When troubleshooting, though, the exact number of troubles aren't the important part; the fact there are any troubles is the important part. Keep in mind there may be many real troubles that have to be fixed one at a time, or there may be only one trouble causing the panel to detect many "troubles".
You say damage, was that lightning damage? If it was lightning damage, a lot of little things could be wrong.
Disconnected for Safety
A device showing trouble could mean quite a few things. Usually, though, a trouble is where the panel is not detecting the device. Once or twice in 20 years, a short occurred between the utility 110 volts and the wires in the fire alarm system. That "electrified" the fire alarm system with 110 volts.
That danger can be checked out by measuring the AC voltage between the loop conductors and building ground. If there isn't 110 Volts AC on the loop, a short like that isn't really on the system. The 110 volts would be the only "true" personal safety concern at the moment.
By Douglas Krantz Check It Out
Reconnect the Loop
Right now, the fire alarm system is broken. The worst personal safety issue that could happen when reconnecting the loop is that the horns and strobes would sound off, and the fire department would be called. That may annoy people, but that's not going to really "hurt" anyone.
Before doing anything else, while actually working on the system, temporarily put the system on test with the monitoring company. While you're working on the system, at least the fire department won't be called.
Then reconnect the loop. When there's trouble on the system, part of a system is better than no system, at least until all the troubles are fixed.
Fix the System
The troubles on the panel are usually caused by the panel not detecting the devices that are in trouble. When there are troubles on the panel, the "Fire Panel" cannot be considered to be a fully functional Fire Detection and Alarm System. Something's not working right, so it might not detect all fires or warn the occupants of the building when there is a fire.
It's a big building and the wires are hidden; you just have to spend some time finding the problems. The bottom line though is you have to fix the system.
Shorted Wires or Class A Troubles
If there's a short on the system, find the short. You have to think it through, but fixing the short may fix all the troubles.
If you're working with a Class A loop, both ends of the loop are connected to the panel. You might have a broken or loose wire. That might explain why you only have 25 troubles right now, but there are 104 devices on the loop. You'll have to think through how to troubleshoot.
Reconnect the loop. Measure the voltage at the screw terminals of the panel where the loop is connected. If it's an addressable system, the voltage should be jumping around. Get used to reading the jumping voltage. It is supposed to be that way.
Now go to one of the devices that the panel says is in trouble. Look for the light on the device to flash its light briefly every second, or 5 seconds, or 20 seconds. If it is not flashing, it is not communicating with the panel.
At the device, measure the loop voltage. The loop voltage should be the same as you saw at the screw terminals of the panel.
If the voltage is the same at the device as on the panel, that means that the wires are connected to the panel. If the device still does not flash when it's the proper jumping voltage, then the device is bad and needs to be replaced.
If there isn't any voltage on the loop, then somewhere, the voltage is being interrupted. Find out where the voltage stops, fix it. Some of the troubles will disappear.
Keep doing the same thing until there aren't any troubles left on the panel. When there aren't any troubles on the panel, the fire alarm system is fixed.