It's established that Jean never truly 'died' at that point and her body was in stasis in a cosmic cocoon. If the soul never leaves the original body it can't inhabit a clone, gemstone, or anything else. Via the magic of retcons, it was established where Jean's soul was all along, and the retcon that made Maddie into a literal clone of Jean rather than a soap-opera level coincidence happened as a reaction to the first retcon.