In my experience, the firearm would be prohibited only if the rifle is actually chambered for the high-energy calibre.
A parallel to that exists in law today. There's a provision under the restricted firearms definition for firearms that become restricted if they have a barrel length under 470 millimetres, plus other technical considerations. The firearm is considered restricted only if it has the short barrel and not if it doesn't.
That's an exact parallel to the situation you're describing. The way the courts have dealt with that is to consider what the firearm actually has mounted in order to assess its classification, so I don't think there's anything in particular for an owner of the type you described who happens to have a spare barrel in a calibre that's over 10,000 joules.