>>56007657On the contrary, being an artificial Pokemon it can be replicated, as long as the requirements for its creation are met*, this was the explanation in-universe for her creation, this Mewtwo was created from fresh Mew's DNA unlike 1st Mewtwo (he was cloned from fossilized cells from an eyelash of Mew) it is implied that her creation was through a research rival of the Plasma team since they was dedicated to the Genosect project.
It was also not a change, the original Mewtwo still exists, he appeared again in PJ, just as BW's Mewtwo also appeared in a special episode recounting her escape.
Now the real explanation was because the Mewtwo from the first movie was registered as an original character by Director Shudo, obviously he does not have rights to the species, but if a Mewtwo is used again with the original voice actor or similar it will be considered an infringement of those rights, to avoid this as much as possible, a female Mewtwo was created with a different personality than the original. Later, an agreement was reached with Shudo's relatives to bring the original Mewtwo in Journeys.
*There is even a Mewtwo from the Sengoku period
