The last record of Kiya comes from a wine label from Amarna. The reason why she disappeared is not know, she may have fallen from favour with the royal court.

There is a relief in the royal tomb at Akhetaten which may provide a clue.

Death Scene from the Amarna Tomb

In this scene Akhenaten and a queen can be seen mourning a body in the lower register, while in the top a nurse (highlighted in red) carries off an infant. The presence of a fan bearer (highlighted in yellow) indicates that the child is royal. If this scene shows Kiya at around year 9 of Akhenaten's reign then the child could be either Tutankhamun or Smenkhkare.
Alternatively, the Queen shown mourning is wearing the crown traditionally associated with Nefertiti which could mean that the person being mourned was one of their daughters.