If they picked the Destroy ending, then the relays would be useless for sure, since no one except the Reapers understand the inner workings of a Mass Relay...although I can't remember if there's a destroy ending where if you max out your EMS, it does minimal enough damage to recover?
Either way, they certainly went out of their way with extended cut to make sure we knew there was a chance the relays could still be used in both Control and Synthesis.
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