From what I've read and an email from Fenner, as I understand it ammonia over 1 begins to kill beneficial bacteria and can harm your cycle. While maybe not "stopping" it, it certainly will hurt it. Plus, as bacteria dies, your cycle gets farther off, killing more bacteria....
Some things don't add up here though.
125 gallons of water at 6 ammonia would not drop to 2 ammonia with a 20% water change. Something is wrong, first off, with either the test kits or methods of testing.
Second, good heavens something died or someone poured ammonia stragiht into the tank. 125 gallons of water going to 6 ammonia is a lot of ammonia... Any chance cleaning solution, windex, etc. got in the tank?
Cleaning the filtration media all at once was a bad idea, but from the bio load I don't think that is the issue. There should have been plenty of bacteria in the rock and substrate to prevent this big of a sudden swing.