Realistically, no. You can drag pages around in the sidebar to match the correct order but it can't be automated, not least because the JS API can't read the action of a bookmark so it has no idea which pages the bookmark is referring to.
Well actually, it can be automated and I have a tool that does exactly this operation at www.pdfscripting.com
While a script can't read a bookmark action. It can execute a bookmark. As long as you are resonably sure the bookmark is a destination, then you're ok. The script runs each bookmark, building up a list of what goes where, and then orders the pages accordingly. My script takes into accound bookmarks that go no where, bookmarks that go to the same location, bookmark hiearchy, and pages that are not bookmarked.
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You don't by any chance have a script that will put bookmarks into alphabetical order do you?
You can export your Bookmarks as single PDFs, and then since all your PDFs are named by their respective page numbers, you can simply combine them into one PDF, and voilà.
How did you export Bookmarks as single PDFs in Adobe Acrobat?
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Easy. This is an Accessibility feature of the Acrobat Pro. You can automatically create bookmarks from a Structure. The Tags functionality enables you to create these Structures.
1. Assuming you have Acrobat Professional (i haven't tried this in Acrobat Reader), go to View > Show/Hide > Navigation Panes >Tags. The Tags pane will show up in the left sidebar. Click in the Options button in the Tags sidebar, and then click Add Tags to Document, like this:
This will create a structure you need. It basically tags all the (physically scanned) pages and creates a document tree. Now you have a logical structure.
2. Now click above on the Bookmarks icon, and click on the Options button. Then click New Bookmarks from Structure, like this:
A dialog window will pop up, like this:
Click OK.Now you have created your Bookmarks (Figures). But the problem is, you can only export Top Level Bookmarks as single PDFs, and this procedure creates only one Top Level Bookmark, under which all other Bookmarks are nested. Not a problem.
3. Simply expand the bookmark, and manually drag and drop all the nested bookmarks above this top-level bookmark, to make all of them top level, like this:
Please note, for some reason, if you select all your bookmarks (Figures) and try to drag and drop them above the top level bookmark, Acrobat Pro only does it for the first two. After that, there is no problem, you can select all the rest, and drag and drop them above this top level bookmark. After you have done this, the top level bookmark doesn't point to anything, so you can safely delete it. Now you have top level bookmarks for all your existing pages.
4. Now you have to rename them, one by one, for example Item_12, Item_46, Item_168, in whichever order you have scanned them.
This only takes a few minutes, even if you have hundreds of pages. After that you use the Split Document functionality, like this:
Here you can split the Document into multiple PDFs. Click on this button, and then this dialog will appear:
Select the Top-level bookmarks radio button. But also click on the Output Options button, and this dialog will appear:
Select Use bookmark names for file names, and click OK. If everything goes well, you have successfully created single PDFs for each of the individual bookmarks, and this dialog will appear:
That's it. Now you can merge your nicely numbered individual PDFs into a single Binder. It is really that simple.
Let me know if you need anything else.
This works only for top-level bookmarks.
Clearly you haven't read my entire reply.