Johan might be the legitimate child since he looks like his mom and dad, while Issac looks only like his dad but with dark hair, he might be the bas****
So she must have married with that wealthy guy and kept her hidden from Shinpei and now he finds out she was alive... or he died and imagined their last moments together and the last part of the letter is fake
If this was a true story,it would have ended with both of them being killed for the atrocity of falling in love with the same gender since it was considered to be a wicked thing. So one of them would have been considered a witch and she would get killed or both of them would choose to die. Thankfully this is is fiction