Run from root partition A and only update on partition B, essentially via chroot. Downtime required for updates is the cost of a reboot. If, however, upon an error during boot, reboot into other partition which will be your last known good config.
Seems simple and straight-forward but is difficult for unmodified Debian-based distributions, so they've addressed this as a key feature of CoreOS.
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"Recoverable system upgrades" - https://coreos.com/blog/recoverable-system-upgrades/
Run from root partition A and only update on partition B, essentially via chroot. Downtime required for updates is the cost of a reboot. If, however, upon an error during boot, reboot into other partition which will be your last known good config.
Seems simple and straight-forward but is difficult for unmodified Debian-based distributions, so they've addressed this as a key feature of CoreOS.