Calibre now creates a backup of the original epub, which it will use on any further conversions (in case you need different tweaks/options for desireable results.).. You can also restore the original from the Meta Data screen. I would nontheless advise keeping a backup of your books as they were before bringing into Calibre. It's a fairly sophisticated program, and it's relatively easy to make oopses.
*Edit* Not discussed here, but it's worth mentioning that using the "Tweak Epub" command to manually make changes to an epub will not back-up the original, but works directly on the current file.