Yes, I would specify it somehow. I would like some input, if anyone knows it, of the best way to do it, considering that I know the ordering of the bookmarks by their names. I also know they point to the correct page, by the pages are also in the wrong order. If I have the bookmarks in the correct order, I can do and Extract Pages, to get them in the correct order based on the bookmarks, and then re-create the bookmarks based on the file header stucture. The only part I am missing is how to reorder an existing bookmark list based on a specif structure.
You can also write a script to automatically reorder the pages based on the bookmarks using the the "doc.movePage()" function. I've written lots of scripts to do this sort of thing. In fact, there is one up at www.pdfscriting.com. It's labeled "Use Bookmarks to Re-order pages"
The source for PDF Scripting Info
Having trouble, Why Doesn't my Script Work?