Hi Mary Pooh,
I use XP so I am not sure how Ubuntu works. I created a separate folder which I "copy" new eBooks into that I want Calibre to import. That way my original is still intact. Just make sure to update the link to this new folder in Calibre so it doesn't continue to go to the ADE folder.
Since I get eBooks from a variety of places and keep them in folders by Store/site it is just easier to have one location for Calibre to import from.
Welcome to Mobileread!