Read this recent article, though:
http://www.zdnet.com/mountain-lions-...er-7000002179/
and the ones it cites.
In general, Mountain Lion saves the original document
with all changes as well as creating a new one when one does a Save As... At that point the new one and the old one are identical. It's definitely not the behavior an experienced user expects. This behavior has been observed in the Apple applications. It may or not be the case with others. I don't have Mountain Lion; what behavior have people seen in Omnigraffle?