What I ended up doing, because this problem has plagued me for months now, is if for some reason I cant break the dependency in the reference viewer I use the Auto Resolve Incomplete Objects, Update with Object on Server, else ignore option in Windchill. It got the file into Windchill without adding ghost objects or giving me a failed upload error in creo.
In my almost decade of using Inventor and Solidworks, I never was not able to break a dependency/external references, the only consequence was that the geometry was then frozen and became a static feature. It worked exactly like how PTC sometimes does when the Break Dependency option is available.
Seems to me that PTC needs to make it so that RMB menu always has the Break Dependency option in the reference view like the similar functionality of their competitors. That would make life incredibly more easy.
