I don't really seem to get this OS thing you're talking about, I just expect that when I choose Save Project As, the newly saved project will contain valid data. Currently, this is not the case, as it points to invalid locations of files. This makes Save Project As totally useless, as it is no more, than a simple file copy operation.
What makes it worse is the fact, that the newly saved (invalid) project is used from this point on.
Also, I DO NOT expect anything to happen to my project file's byte representation when I copy with Explorer for example.
If the Save Project As menu entry does nothing else, than a simple file copy operation, why is it even there?