Thanks for the reply. I know the mechanics of how to break the references. But I don't know where to break the references.
To better explain, components involved are:
I'm not editing the PCB or connectors, but using them to create cutouts in the enclosures. Ideally, I'd have Assembly (old)/Enclosure (old) linked with external references, as well as Assembly (new)/Enclosure (new) linked with external references. I think this should be possible since the common components aren't being changed.
I think my problems come from the fact the Enclosure (new) was built from and then a 'save as' from Enclosure (old), so maybe it inherited the external references?
If I break external refs from Enclosure (new), then create the cutouts from the connectors, will it add new external refs to the connectors? (this is what I want to happen).
What about using "Replace Components"?
1.File > Save As Copy & Open to save Assembly-old as a new name (Assembly-new)
2. In assembly-new, right click on Enclosure-old part and select Replace Components. Browse to Enclosure-new and select the "re-attach mates" option.
This is the point I'm at now and stuck (I'm working on some other stuff so haven't had a chance to play around). It's now (within Assembly-new), when I try to use the connectors to make cutouts in the side wall of Enclosure-new I get the errors.
This is the reason why old references must be broken: to let you replace unwonted inherited with a new ones.
I would break all listed references to old assembly. Worst keys scenario you will have to create a couple extra references or just add a new dims if new assembly becomes unstable.