There are some threads in the web about this issue, but nothing on how someone fixed this problem. So I document it, since it still is fresh in my mini brain. 
I got this Yamaha P2250 out of the bin yesterday. Air dried it until today, checked a few things inside while it was drying (rectifiers, caps, other diodes, finals, drivers etc). Couldn't find anything wrong, so I did the AC light bulb in series trick and fired her up.
I am just kidding. 
The protected and the channel A clip LED were on and she didn't want to get out of it.
Frigg me... 
so I checked all the output transistors and drivers again. Nothing wrong. Checked the DC offset and it was within spec. Downloaded the service manual and thought, maybe the temperature protection is on. That was not the case either. 
So I took the whole power module A out and tried to run the amp with the power module B only. That didn't work as the amp was is protect mode again, even so there was no DC on the test point or anything on module B. 
So I decided to let her warm up some (took 15mins for me until the idling current adjustment stabilized). Set the idling current on module B for 12mv. I tried to fool with the protection circuit and no dice. Then I put power module A back into amp and hooked everything up again, trying to compare voltages between both modules and do another test on the protection circuit. Fired her up and? She worked! 
No more clip A and protect mode. So I let her warm up again for the idling current to stabilize and set Power Module A and again on B for 12mv. Amp is working good so far!
That thing does 170wpc
I got this Yamaha P2250 out of the bin yesterday. Air dried it until today, checked a few things inside while it was drying (rectifiers, caps, other diodes, finals, drivers etc). Couldn't find anything wrong, so I did the AC light bulb in series trick and fired her up.
I am just kidding. The protected and the channel A clip LED were on and she didn't want to get out of it.
Frigg me... so I checked all the output transistors and drivers again. Nothing wrong. Checked the DC offset and it was within spec. Downloaded the service manual and thought, maybe the temperature protection is on. That was not the case either. So I took the whole power module A out and tried to run the amp with the power module B only. That didn't work as the amp was is protect mode again, even so there was no DC on the test point or anything on module B. So I decided to let her warm up some (took 15mins for me until the idling current adjustment stabilized). Set the idling current on module B for 12mv. I tried to fool with the protection circuit and no dice. Then I put power module A back into amp and hooked everything up again, trying to compare voltages between both modules and do another test on the protection circuit. Fired her up and? She worked! No more clip A and protect mode. So I let her warm up again for the idling current to stabilize and set Power Module A and again on B for 12mv. Amp is working good so far! That thing does 170wpc