I don't do Cerakote, but I've done quite a bit of GunKoting the past year. I always tear everything down to its smallest parts and bead blast then kote and bake them. Minimally, I would remove the trigger assembly and any plastic parts from the action and barrel. You likely can get away with keeping the barrel and action together so as to not have to worry about removing (or, more importantly, replacing it).
But, regardless, whenever you remove the barrel it must be re-checked for headspace. Some guys will put a sharp cut or scratch mark to serve as a witness mark in the nut and barrel so you can just tighten / turn the barrel and nut down so they are close to the same place using your previously fired brass as a gage and then further turn it till the witness marks line up again. I have never done so, but I assume it would work. It makes sense that it would. Certainly would want to make your mark on the underside of the barrel. There's no need to worry about head spacing just b/c you tear down the bolt assembly, though. That won't change anything if you reassemble the same parts. Just if you remove the barrel from the action or replace the bolt head or bolt with new parts.
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