When the tomb was discovered, in 1907, it was found to have been ransacked and desecrated. The shrine for enclosing a coffin had been dismantled and pieces scattered everywhere. Names had been erased, but not everywhere... some traces remained, and those have served to complicate the problem even more.
In fact, there are traces of the names of Amenhotep III, Akhenaten, Tutankhamun, Tiy, Sitamun (a daughter and wife of Amenhotep III) and the enigmatic Kiya (who is believed by some to have replaced Nefertiti late in Akhenaten's reign).
The shrine appears to have been made for Akhenaten's mother, Tiy, who is thought to have been originally buried in KV55. The shrine appears to have been abandoned when it proved difficult to remove, probably when Tiy's mummy was removed.
The tomb also contains the magical bricks of Akhenaten, arguing strongly that his mummy was interred here at some point.
It appears that the coffin itself was designed for Kiya, but later modified for a male occupant, by the addition of a fake beard. But the cartoche bearing the name of the occupant has been cut out, and the face mask ripped off.
The mummy contained within the coffin has not made the problem any simpler. It is male, but opinion is still somewhat divided on the age of the corpse; more recent examinations [1] have suggested a younger age around 20, too young for Akhenaten, but there is some evidence that these age estimates are not very accurate. Some have argued that it is Akhenaten himself, while others suggest that it is Smenkhkare.
One possibility which has been suggested, if the mummy is indeed that of Smenkhkare, is that the tomb at one point held Tiy, Akhenaten and Smenkhkare; when it was later opened (possibly as a result of being discovered during the excavation of KV6, the tomb of Ramses IX, immediately above it) two mummies were removed, with the intent of leaving the heretic's desecrated coffin, but a mistake in identity was made.
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