I think I already know the answer to this one...I have a 200+ page document with a bunch of hyperlinked PDF ads in them. When I export the .PDF, the hyperlinks are gone, except for e-mail addresses and URLs with "www." This also happens when I place the original InDesign document instead of the .PDF. Is there any other way to maintain the hyperlink, or am I going to have to add a hyperlink manually in InDesign or Acrobat Pro?
If you have the original INDD you can use the content tools to transfer (and link) content from one document to the other. But be aware, as they are now open files, you should put all styles in a subfolder to avoid messing up styles. Different baseline grids may also cause problems.
Important is, that the other document has either a different layer name oder exact the same layer names in the same order. The content tools will not catch content from a master/parental page if you take it from the page.
What you experiencing with working text links, emal addresses and URLs, is not a transfered link, it is an automatical link detection in you testing setup. Not every other user might experience this.