@amz - the other question that should be asked is why are you "adding them back in"?
If you have already cleaned up the metadata in Calibre before saving to disk, what do you think adding them back in will achieve?
If you are just trying to create a clean library, use the Copy to Library function to move the book from your "in progress" library to your "clean" one.
Or is there some other cunning reason I am missing...