Tim has posted an excellent piece of detective work regarding the identification of the mummies of Tuthmosis I and II, well written and intriguing, it poses a lot of interesting questions and gives a lot of information about the post mortem travel arrangements of New Kingdom mummies! Tim also includes a short list of references at the end of his post. Here's a short exerpt:
It is an assumption that upon the death of Hatschepsut that Kv20 would have been filled with the two royal mummies and closed. Unknown at which time the burial of king Hatschepsut was dismantled perhaps at the end of the new kingdom or at the time of removal of Thutmosis I, that is if Thutmosis I actually ended up reburied in Kv20?
His quartzite sarcophagus was found lying on it's side, a position more attuned to be an accident of descent into the tomb rather than a necessity of removal of his coffins. The thought that robbers to the tomb would turn the stone sarcophagus on its side would have taken allot of manpower for a pointless act. Especially given that the tomb robbers probably worked very fast to get in and out of the deep dangerous tomb they were robbing whether clandestine or state sanctioned.
Rather I cannot help but feel that Thutmosis I's mummy never re-entered Kv20 but more than likely remained in the tomb Kv60 throughout her reign leaving Hatschepsut's intentions unmet at her death.