Information Technology Reference
Running Backups from a Duplicate
Ordinarily, you'll run your Mac from the duplicate for only a few
minutes—just long enough to verify that everything worked correctly.
But what if, while you're booted from the duplicate, your versioned
backup software runs automatically? (I'm thinking in particular of
CrashPlan, because it normally runs continuously in the background.)
Won't that cause problems?
Short answer: no.
Since a clone is an exact duplicate, your other backup software can't
tell the difference between a clone and the original volume. It also
can't tell whether you intend to continue running from the clone, or
whether you might want to avoid backing up when you're running
from the clone. So when your backups start again while you're
booted from the clone, they'll pick up with any changes made to the
clone. This is normally a good thing, because you might clone your
drive in order to move to a bigger disk, or replace a dead disk, or
whatever, in which case you'll want the new disk to behave exactly
as the old one did.
If you create or change files when running from the clone, your
software should back them up, and if you later go back to using the
original drive, it will notice that some things don't match. That might
prompt it to rescan your disk and take some extra time to update
your backups, but it won't delete those recently backed up files, so
all your data should be safe either way.