I doubt Megas are going anywhere, not after they wrote dex entries for the megas of pokemon that show up in the Alola dex. Any mega outside of the Alola dex might disappear if any are being removed at all>>31647842They're a stubborn Japanese company, and the literal Pokedex numbers are probably seen as a vital part of the Pokemon brand that they'll never reorganize the national dex, much less remove two slots by making the Nidoran lines count only as one species with very unique gender differences like they were conceptually intended to be, and like how the Meowstic line actually works in-game.
A "Crisis" would be just some big showy event that marks that everything published after that point has had the canon trimmed and reorganized to better suit new consumers to the brand and new content to be made, instead of carrying around a messy history of separate inconsistent canons
For Pokemon, it could be
>rearranging the National Dex to account for new mechanics, cross gen evos, and Pokemon released in later gens that interact with older regions>potentially removing pokemon entirely>changing how Pokemon evolve or have form changes to better suit future games, like Feebas and Prismatic Scaleetc.