Board Thread:General Discussion/@comment-28128661-20160404143233/@comment-27701762-20160418060340

I wasn't referring to whether Alphys knows that Flowey is Asriel and so on. Simply to the speculation you had that Alphys replanted or returned the flower to the garden.

There may be a hint that Alphys is aware of Flowey as a sort of malevolent talking flower or something along those lines, since she seems rather shocked when Papyrus mentions that a talking flower told him to gather everyone.