The OP is probably referring to the part of Bendis's last Invincible Iron Man run that introduced the highly despised middle-aged rocker star mom Amanda Armstrong. When she was younger she was recruited by SHIELD but IIRC she retired. Not only did Bendis change the mom, he changed the dad to a Hydra double agent that infiltrated SHIELD who had an affair with Amanda. They had a baby and he was adopted by the Starks and named Tony. Yeah, I think this whole retcon should be tossed out but not for the reasons in the OP. It's just completely stupid and unnecessary.