Make a new backup whenever you make any important changes in the webUI. Go to Main - Boot Device - Flash - Flash Backup to download a zipped backup of flash. The CA Backup plugin will also let you schedule backup of appdata, libvirt, and flash.
The OS doesn't actually run from the flash drive. The flash drive just contains the archives of the OS. These archives don't change except for upgrades, and are unpacked fresh at each boot into RAM. The OS runs completely in RAM. Settings you make in the webUI are stored on flash so they can be reapplied at boot.
Think of it as firmware except easier to work with and unbrickable.