It's going to be put in the same directory as the original file. Be aware that this is not a replacement of the feature to export files. It just means you can replace the existing PDF with one where the page order is flattened (i.e. if you repeat the first page three times, for example, the new PDF would have three copies of the first page). This means you can do things like embed annotations in each of those pages without any conflict, whereas you can't do that when utilizing the page order, as the same PDF page is used in each instance.
Mike
Mike