Thanks very much to Jen Mason for the following artilce. On Zahi Hawass's own website, Hawass argues in favour of a mummy located in the Cairo Museum being that of Hatshepsut. The first part of the article is historical background information into Hatshepsut herself
There then follows a description of KV20, the tomb of Hatshepsut, and nearby KV60, where Carter found two elderly mummified women (one inscribed for the Great Royal Nurse Sitre-In) and stuffed geese.
Hawass then suggests that the long-forgotten coffin and mummy inscribed for the Great Royal Nurse, removed from KV60 by Ayrton and Davis in 1908, and eventually located after a search on the third floor of the Cairo Museum, were in fact never supposed to be paired together: "The badly damaged coffin is typical of the 18th Dynasty. Among the remaining inscriptions is wr Sdt nfrw nswt In, 'great royal nurse In'. The mummy inside is about 1.5 m. tall but the coffin is 2.13 m, suggesting that the coffin was not originally intended for this mummy. The obese mummy still in the tomb is significantly taller, and would fit much better in the coffin." He goes on to describe the mummy and suggests that her appearence, the quality of the mummification process and the very fine linen used argue that she may have been royal. He points out the the linen on the base of the coffin, not connected directly to the mummy, was of inferior quality.
Putting all of this together, Hawass suggests that the mummy of Hatshepsut was removed from KV20 for security reasons during the Third Intermediate Period, and that it was reburied in KV60 in the coffin of Sitre-In. He beleives that the mummy currently still resident in KV60 may have been the original occupant of the coffin.