From the conclusion of a general sort of piece on Cleopatra in a science column at ABC:

Napoleon Bonaparte looted many treasures from Egypt, including the mummy case of Cleopatra VII. Most of these treasures were returned to Egypt, but her mummy case was accidentally left behind.

In the 1940s, workers found her mummy case, and emptied it into the sewers. Sad to think that a dirty French river should be the final resting place for the Queen of the Nile.

Hmmm ... another story about Cleopatra's mummy case (compare this one); this one has 'urban legend' written all over it, I suspect. The only source I can find for it seems to be down at the moment ...