More like it’s still canon, but heavily retconned. FRLG removed some of the early weirdness and made it more consistent with the others, and Let’s Go removed what little they missed with the first set of Kanto remakes. Both versions of Johto are direct sequels to Kanto, everyone important in the region shows up to the world tournament in B2W2, and Red and Green/Blue appear as adults in Sun/Moon’s post game. It’s just the references to real world countries and animals and stuff that they sweep under the rug and say “You didn’t see that. That didn’t happen.”