Hi there,
I found a bug where when you would add a new site to MainWP and click on Install BackWPup plugin and Apply BackWPup settings (see here) it will only install the plugin on the new child site, but not sync the existing backup jobs.
If you switch to the BackWPup extensions tab, click on a backup and then on Save Changes (see here) it will sync the job correctly, so at least there’s a workaround solution.