We have previously highlighted the unexpected behaviour of “Save As…” when Apple brings back the feature in OS X Mountain Lion. Turns out that Apple is listening, and “Save As…” behaviour is improved to the sane way starting with OS X Mountain Lion 10.8.2.
In OS X Mountain Lion 10.8.0 and 10.8.1, when you “Save As…” an editing document to a different file, all the changes you made will automatically be saved to the original document.
In OS X Mountain Lion 10.8.2, the “Save As…” window has a new “Keep changes in original document” option.
When the option “Keep changes in original document” is not checked, the original document will revert back to the last saved version, and the new changes will be in the new saved-as document. This is akin to what we would have expected from the “Save As…” behaviour.
If you would like the changes be saved back to original document when you “Save As..” to a different file, just check the “Keep changes in original document” option.