Indd CC does not keep bevel effects on a compound path shape when exporting 1.4 pdf and above.
Only work around seems to export as a flat 1.3 which is not an option because of spot colours underneath it.
Having to rebuild it in illy
Where did you check your exported PDF? In Acorbat or Reader it would be ok, but don't try to use Preview or other non-Adobe-PDF-Viewer, they will not show correct PDFs, they are trash when it comes to show PDF1.4 or higher.
Don't stick with 9.1, upgrade your InDesign.
But if you use spot colors combined with transparency it will in most cases (exceptions are some combinations with multiply) be converted to process colors, it doesn't matter if you flatten it or not. Have a look in Output Preview (available in InDesign and in Illustrator).
Ok, I have tried with your file. These forms are wired, but I could repair it.
Never—NEVER—work without styles.
Now you can export the PDF and it will work (at least in Reader and Acrobat).