what kind of damage are you refering to?replace the rotating SCR heat sink assembly (on the rotor, inside the gen end....NOT fun or easy) and the rotating photoboard on the end of the shaft. (not fun or easy). in theory you can test them and replace one, buuuut.... High voltage with a taped over photoboard means one or both is bad....unless someone might been elbows deep in there and played with the wiring....
Your AVR has nothing to do with the issue.
This is kinda NOT a job for the inexperienced. You could do permanent damage to the generator end if you are careless.
If the phototransistor is covered with electrical tape and you're getting any voltage at all other than residual (a few volts AC) either the phototransistor board has failed (not common) or the SCR assembly on the rotor is shorted.
If I was a betting man I would say you have a bad SCR assembly. It can be checked with an ohmmeter when it's disconnected from the phototransistor board to confirm, but you might as well pull it.