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.