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Without knowing the details of the car, I would design a fuse or a circuit breaker between the main positive of the battery and the primary distribution point. I'd then fuse/breaker each of the main sub branches, then each circuit after that, etc.
It's possible to use an electronic/auto-reclose circuit breaking device, and pulling the main lead could be the reset mechanism. It's likely that even if the starter had power, the control power for the solenoid relay was out.
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