If you save a copy of a document you’ve made changes to, OS X 10.8 Mountain Lion will just add your changes to the original document, and when you close the file, save the changes.
There is a way to recover, you can manually use Mountain Lion’s versioning feature to revert to the previous version, but that’s a manual solution, and if you open a document expecting to see one set of info, and you see a different one instead… Well, that sucks.
Until this gets figured out, it might be a good idea to go back to just duplicating a document and making the changes there. We’ll keep you posted if we hear of a way to make “Save As” work properly under Mountain Lion.