Rest assured, at least all german military aircrew fly on military licenses rather than a CPL / ATPL (H).
You can, however, convert your military to a civilian license reasonably easy, on your own cost of course and depending on your flying hours on multi-engine helos.
Helicopter training in GER is orientated along the JAR requirements of a CPL however and therefor fairly easy to convert.
@Hueymeister: Do you work near Rendsburg? Know Lars B.? Also here in GER?
Thomas