Your waterflow switch is an assembly consisting a paddle across the entire inside of the waterpipe, a lever assembly to push on a switch, an air damper (retarder) to keep the lever assembly from releasing the switch for :45 seconds, and the switch itself.
When water moves, it pushes on the paddle, the paddle pulls the lever assembly, and after :45 seconds, the air damper allows the lever assembly to release the switch. When water is moving into the sprinkler system for more than :45 seconds, there is an alarm. If water doesn't move, there is no alarm.
You've replaced the switch, so we can assume the switch works. You replaced the panel and wiring, so that works.
I'm not sure how the check valve was pressure tested, but that testing was probably tested during the day, when the temperature above the ceilings was higher than at night. Temperature is very important to the false alarms.
If there's rust inside the pipe, making the surface very rough, there is the slim possibility that the paddle gets stuck in the alarm position. The water might flow past the waterflow switch assembly for only a few seconds, but then the paddle may stick on the rust for a couple of minutes, and then send in a false waterflow alarm. It happens once in a while.
You've bought a bottle of pop from a convenience store. At the top of the bottle of pop is air. In a sealed pop bottle, the air doesn't go away, it is still there after years.
When the sprinkler system is drained in order to work on it, water is let out of the system. In order for the water to come out of the whole system, air has to be let into the whole system. When water refills the system, the air is not let out, the air is only compressed to make room for water.
Yes, some of the air will be absorbed into the water, but that partial absorption can take years. Yes, many times there are microcracks at the pipe joints, small enough to hold the water in, but the air being thinner, can slowly leave the system. Letting the air out that way can also take months to years.
No matter what anyone says, unless the air has been deliberately bled out, there is air in the sprinkler system.
Even though the "Code" says to install bleeder valves in a sprinkler system, most of the time the bleeder valves have not been installed. If bleeder valves have been installed, the bleeder valves will be somewhere at a high point of the sprinkler system, above the ceiling. They're not easy to find, and sometimes not easy to even get to.
Pressure Tank Temperature
The sprinkler system is a long, thin, pressure tank. There is air in the tank, and there is water; air compresses, water doesn't; if the air pressure increases or decreases, the water pressure increases or decreases to match.
Air pressure in the sprinkler system changes from day to night. During the day, when the sun is out and the space above the ceiling is warmer, the air pressure is higher; during the late night, when the sun has not been shining for a while and the space above the ceiling is cooler, the air pressure is lower. In the winter, the space above the ceiling will get cooler at night than during the summer. That seasonal difference means the air pressure on cold winter nights will be even lower.
City water pressure changes from day to night. During the day, when lots of people in the community are using water, the city water pressure is lower; during the late night, when few people in the community are using water, the city water pressure is higher.
When the city water pressure becomes greater than the sprinkler system pressure, water is pushed into the sprinkler system - past the waterflow switch. The most probable time for this is at night, when the city water pressure is highest and the sprinkler system pressure is lowest. That's why the false alarms happen at night, not during the day.
Bleeding the Air Out
Bleeding the air out will allow water to come into the system to replace the air as it is bled out. You will have false alarms at that time. If your system even has bleeder valves, you probably want to leave bleeding the system up to the sprinkler company.
The bleeder valves have to be installed in the first place. There is a good possibility that the bleeder valves were never installed. The sprinkler company, for its part, can't bleed all the air out. Some air will stay in the system no matter what is done. Bleeding some of the air out may reduce the false alarm problems, but bleeding only some of the air won't fix the problem entirely.
The inspector's test valve is almost never installed at a high point. The purpose of the inspector's test valve is to see if water flowing in the system will set off the alarms. If you open that test valve, you will set off the alarms. Just don't open up that valve.
It's the Water Leaking Out
If one time, after the sprinkler system has been drained and refilled, you have water pushed past the waterflow switch and have a waterflow alarm, OK. That means that the flow switch is doing its job. Water has been pushed in past the check valve and into the system.
Once enough water has been pushed in so the pressure in the sprinkler system has more pressure than the city will ever have in their system, there should never be another false alarm.
Repeated false alarms, though, is a different matter; repeated false alarms may be triggered by pressure changes, but repeated false alarms are caused by water leaking OUT of the sprinkler system. The sprinkler system has a limit to how much water it can hold, water has to be let out before more water can come in.
Water could be leaking out of a sprinkler pipe or sprinkler head somewhere. Store owners, however, would complain if that were happening.
The drain valve or inspector's test valve could be leaking. That can be seen by looking for water dripping out of the sprinkler drain pipe. The water leaking though a leaky valve has happened several times. False alarms from leaky valves have occurred once a day to once every several weeks. To see if this is a problem, look at where the water comes out of the sprinkler drain or an inspection valve. If the insides of the drain pipe is wet, or worse, dripping, the valves may be leaking.
Water could still be leaking backwards out through the check valve. Pressure testing during the day will show how the system is working while sun is shining, not at night when the sun is down. Don't rule out the check valve leaking, that is a hidden problem.