That second Mewtwo movie IS "Mewtwo Returns"
Since that movie has a "Made in Amerika" all over it, it's not official. Thus, no events in that movie can be considered part of the story line. Therefore, that movie never really happened. 4Kids and WB probably just got bored.
You can check Bulbapedia.
You're confusing "Mewtwo Returns" with "Mastermind of the Mirage Pokemon". This is what bulbapedia says:
The first Pokemon movie (Mewtwo Strikes Back)
Premiered on July 18, 1998 in Japan first seen in North American theaters on November 10, 1999. See
https://bulbapedia.bulbagarden.net/wiki/Mewtwo_Strikes_Back.
Ash and co's memories got wiped clean here at the end of the movie.
Mewtwo Returns
Broadcasted first on the Japanese television on December 30, 2000. Released on DVD in the US on December 5, 2001. See
https://bulbapedia.bulbagarden.net/wiki/Mewtwo_Returns
This is
NOT a movie. 4Kids called it a "Movie Adventure", yet it was never shown in theaters. Not in the US, nor in Japan. So you can thank the boys and girls from the 4Kids marketing department for the confusion they created.
This TV-special is thought up and made from start till end in Japan, so this is official as it can get.
Ash and co met Mewtwo in the TV-special and Mewtwo was about to wipe everyones memory clean once again. Everyone including Mewtwo agreed in the end that
forgetting things doesn't mean that it never happened. So Mewtwo only wiped clean the memories of those that were outside (Team Rocket, Luna Carson and Cullen Calix).
Ash and co still remembers Mewtwo.
The Mastermind of the Mirage Pokemon
First broadcasted in the US on April 29, 2006, and was broadcast as streaming video from the TV Tokyo Anitele web site from October 13 to October 31, 2006. See
https://bulbapedia.bulbagarden.net/wiki/The_Mastermind_of_Mirage_Pokémon
Like "Mewtwo Returns" this is NOT a movie, but a TV-special. Made upon request of PUSA.
It is debatable if Mewtwo's appearance should count as being seen by Ash in "The Mastermind of the Mirage Pokemon". But Ash already met Mewtwo in "Mewtwo Returns" and still remembers Mewtwo.
So after a long detour the anwser to the question "has Ash seen Mewtwo?" should be "yes".