Why do we assume Wanda (Pietro, Tommy and Billy for that matter) aren't back up? if this plans was being hatched for years and the retcon that they're not mutants probably happened only a few years in universe, what's to say that a record wasn't being kept before the reveal? or even after, since we saw that clearly Magneto had conflicting feelings about it no matter what he may have said in public.
Science and tech id-ed her as a mutant for decades, it would be weirder if they didn't have a back up her.