I just re-watched Mewtwo Returns the other day, and in the end Mewtwo erased Giovanni's memory. But I'm wondering if Giovanni has completely forgotten Mewtwo?
Two reasons why I don't think that he has:
1. It wasn't indicated whether Mewtwo completely erased all memory of his existence from Giovanni, or just the memories of what occurred at Mt. Quena. It's possible that Giovanni has forgotten the events of the movie but still remembers everything that happened prior to The Battle of the Badge and the first movie
2. Even if Mewtwo had completely erased Giovanni's memory... Giovanni most likely has records of Mewtwo's existence as well as a lot of the research data that was not kept on New Island (and was not destroyed by Mewtwo)... so even if Giovanni had forgotten he could simply refresh his memory by looking through his records
Either way, I doubt that they'll ever make it into a plot point. Which is unfortunate because Mewtwo's one of my favorites...