BackBlaze will not TOUCH anything only on iCloud (or network storage), period. It backs up your local hard drive content (minus macOS, apps, and temp files). They are very clear about this:
This is why many of us do not use Optimized iCloud Storage, and why we also clone our drives with an app like SuperDuper! or Carbon Copy Cloner. (With a cloned-backup system drive you’re back up in a matter of moments if your main macOS drive dies, for example, and with a clone you also don’t have to re-download apps as part of a restore.)