I found this question on Twitter. Short answer: Carbonite checks this in the background using something called a checksum. As amazing as it sounds, about every 90 days Carbonite goes through every one of the roughly 25 billion files we have backed up and checks to make sure that the file in our backup still matches what's on your PC bit for bit.

If you are still feeling nervous, try this: Pick any backed up file on your PC (it will have a green dot on it if it's backed up with Carbonite). Delete it. Now open the Carbonite Backup Drive from the icon on your desktop. Find the file you just deleted – the status column will say "Right-click to restore latest backup copy (Original file deleted)." Right-click on the file, and select "Restore." In a few seconds, you'll see a Carbonite pop-up saying that the file has been restored. Go back to your C: drive and open the restored file. You'll see that it's perfect. I'm sure this is true of every file on you've backed up with Carbonite.

— Dave
CEO, Carbonite