John
Usually for a c of a, not only has the aircraft/component have to conform with the appropriate TCDS but also it has to be proven that parts/components have a civilian regulations conforming maintenance history.
In recent years, I have done both, installation of military surplus equipment on civil aircraft as well as convert military operated/registered aircraft into civil register under EASA guidance.
In both cases, not only conformity to civil TCDS/component records had to be proven but also that all parts/components and the aircraft itsself was maintained conforming to civil standards. Whatever could not be proven compliant had to be overhauled by an EASA approved shop in order to get civil paperwork.
I guess it also depends on how deep the agency or its folks dig into the paperwork when they inspect the aircraft to issue a new c of a.
Regards,
Daniel