I am having problems with hyperlinks not working (on a Mac - Yosemite). I create a document in InDesign with hyperlinks. Export it. When I open it in Acrobat and optimize it, the hyperlinks quit working. Here are some of my settings:
Discard Objects - Only these are checked: Discard all alternative images. Detect and merge image fragments.
Discard User Data - Only this is checked: Discard hidden layer content and flatten visible layers.
Clean Up - Only this is checked: Optimize the PDF for fast web view.
ALSO, I need to be able to secure the document with a password so that it can be printed but NOT edited. However, the hyperlinks will still need to work after it is secured.