Maybe during Endgame he notices the nature of Wanda's power, and when she eventually loses that he tries to help her get her powers back through magic as he knows she got some experience with it, even if unknown to herself. She got them before but she got no professional training like him, with his help and Agatha's she could learn other spells beside her usual energy blasts, shield & tk. Him training her in the second film would also be there to show to anyone who might have missed the streaming series that Wanda learnt magic.
I get that since it's true to her comic book version, but I'm not sure if that's the way to go on the MCU, I don't think a magic background fits the character, it makes more sense for her magic to be related to her connection to the mind stone than a ancestral power. If she does get magic I see it as something that happens going forward, not by changing her past, specially since in the MCU anyone can learn magic.