I don't know if this is the problem, but it has stairs above it, not below it. You found two GVs?

It probably moved when you tried to polymorph it, because the game doesn't want you to poly a big boss like that. As for the stairs thing... that doesn't make sense too much, because the stairs are part of the level, have nothing to do with Genetrix, as far as I know. Maybe someone with more dungeon building experience can correct me...