**EDIT: CS6 To the rescue! The CS6 Interactive PDF Export offers a Pages or Spreads selection option. Hallelujah!**
I have a 500 page InDesign file that I made in CS4 that is intended to be both printed and used in Acrobat with interactive features, including hyperlinks, bookmarks, and buttons. In CS4 I was able to export print and interactive versions of it perfectly. However, CS5′s new PDF export is split into different dialogs for print and interactive, and neither one of them provides the necessary functionality.
CS5′s PDF(print) export dialog allows bookmarks and hyperlinks, but does not allow buttons to function (it has options to either exclude them or include their appearance only).
CS5′s PDF(interactive) export always exports your document as spreads if you have facing pages turned on! After searching around I found a script on InDesignSecrets.com that can turn off the export as spreads, so that the PDF(interactive) export will create single pages for a facing pages layout. However, I discovered something that is not documented on InDesignSecrets, or anywhere else that I could find:
If you use the script to turn off the export as spreads feature then ALL BUTTONS DISAPPEAR FROM THE EXPORTED PDF!
I tested this in a simple new InDesign document after resetting my preferences just to be sure. I’ve also tested it in CS 5.5 with the same results. If you have any buttons in your file and you export using PDF(Interactive) after using the script to disable the export as spreads option, your buttons will not be included in the PDF. Use the script to turn spreads back on, and the buttons reappear.
So the only option now is to make two versions of the file. The online version will have facing pages turned off and I”ll make an updated master page for it that is the same on every page. The print version will be in facing pages.