Mountain Lion's "Save As…' Is Broken
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After the release of Mac OS X 10.8 aka Mountain Lion, there were quite a lot of people who were happy about getting the "Save As…" command back after it has been removed from OS X 10.7. A few days in, it turns out that this command is broken and doens't work correctly. In short: When you "Save As…" a new file, it overwrites the original as well.
This article on macperformanceguide.com explains more details.