It seems like if they aren't sure a high priced part is faulty, they ought to have a test jig to attach it to. The customer bike should not be the only platform to determine if something works or not.
The worst they could do is have some central Zero shop, where suspect parts could be overnighted by the dealer and Zero could have representations of all motorcycle models. Not actual motorcycles, but assemblies for testing that represent the motorcycles, where all the parts can be plugged in and out easily. That way if they aren't going to break out voltages and signals for troubleshooting but merely use rote part substitution to solve issues, they can be sure parts are faulty before they ask you to pay for them.
It sounds like they told you to pay for parts to install that did not solve the problem. That's how I read it anyway. If that was the case, I would be VERY upset. If you are buying parts, be sure to tell them you want your old ones back, no matter what happens.