what you're basically saying is that your sets were on a CM that didn't have DSPs that could serve them.
Follow the alarm logs to see what failed where when. If data center A has a core CM in NR1 and data center B has a ESS in NR 250 and a site happens to be NR1 and location 1, then if gateways and sets from that location all happened to be on the ESS like you said, and with direct WAN from 250-->1, then there's no reason the ESS wouldn't set up calls the same way the core CM would.
Something else happened to make those phones do what they did. Maybe someone goofed a routing change and it made your gateways in some core VLAN unable to reach the main CM and hit the ESS and perhaps that change didn't affect voice vlans that your phones are on. That could have your phones still on the core CM with no DSPs which would explain being unable to make calls.
In system-parameters ip-options, I believe there is an option to 'force phones and gateways to active ESS/LSP' so that if some parts of your gear can hit the core+ESS but other parts only can hit the ESS, the main CM can tell whatever's left on it that those things should go to the ESS because it's 'healthier' than the core. That would be based on the idea that some of your stuff could still actually hit the core CM to make it worth telling them to go to the ESS instead.
You've got yourself a fine mess to deal with. A right proper audit is in order to explain exactly what you've got and I'm sure it would identify some pitfalls which it sounds like you unfortunately fell into over the weekend.