I keep all my originals in its own library. I then have a separate library for conversions which are Mobi and Epub. I can't begin to count how many times I'm half way through a book to find something wrong that needs to be fixed.
Not to mention you never know when it's going to be that one version of Calibre where there is a bug introduced and you just happen to do alot of converting only to find out later you need to go back and reconvert that batch now the bug has been fixed. So having originals are important.