Cross Reference Problems - same document / different document

I have a booklet that has a lot of cross references. It is a renamed InDesign file, but I have updated all of the links to point to the correct document.

When I send it to PDF, some of the links are correct and some still point to a different document. (But it's really the same document.) They appear to work properly when I open the file in Acrobat, but they do not work when the file is send to a flipbook plug-in. (Two different plug-ins were tested - it's clearly a problem in how InDesign defined the links when sent to Acrobat.) 

When I go to Edit Link in Acrobat, good links look like this:

Bad links look like this:

Edit doesn't let you change the action to "this document." (Plus, so many links are affected this would be a lot of work.)

Here's a link to the file in a flipbook. If you go to page 47, you will see that "Amuka" is the only film that actually links. All of the films should. There are problems on the next page, too.

http://design-on-call.com/frff-program-spreads-schedule/

HELP! I have tried everything I can think of. 

Thanks!