It's possible that even The Doctor didn't know about the "forgotten" Doctor if whatever he did was so bad then maybe The Doctor erased his own memory of him and what he did to lock that Doctor away but going into his own time stream unlocked the memory and released him.
I know that could take away from the Doctors greatest secret but maybe he knew he had wiped a memory and knew if he did it to himself it was something that could never be found out not even to himself.
I also know that if he ended The Time War he has spoke about remembering it in the past but he could have also implanted a false memory of that.
It could also be maybe whatever he did came after that what if that Doctor couldn't stop fighting and found he liked killing so killed innocent people inc a companion to a point where his past versions/his good part forced a regeneration onto him inc a memory loss.
I know that could take away from the Doctors greatest secret but maybe he knew he had wiped a memory and knew if he did it to himself it was something that could never be found out not even to himself.
I also know that if he ended The Time War he has spoke about remembering it in the past but he could have also implanted a false memory of that.
It could also be maybe whatever he did came after that what if that Doctor couldn't stop fighting and found he liked killing so killed innocent people inc a companion to a point where his past versions/his good part forced a regeneration onto him inc a memory loss.