I think you are running into a problem that existed in Xway b2 and b3. This meant that resources that were selected in the Link dialog didn't get saved correctly. If you added a resource link, it would work fine until you saved and reopened the document. We fixed this problem in Xway b4.
You should be able to fix this in your document by opening it in b4 and re-setting each resource link:
1. Place a cursor in the link
2. Click on the Resource popup (which currently says "None") in the Link Inspector and choose "Other..."
3. Choose a (PDF) resource from the file dialog
If you save and reopen your document after doing this, you should find that the links have been saved correctly!