The app is generated successfully using PhoneGap and loaded onto an iPad running iOS 9.1 and the hyperlinks do indeed work. However, there is no back navigation button once the link is chosen and a new page is launched. This is either when a PDF baggage file is opened or a link to an outside source such as youtube is chosen. I have tried changing the link options to display in Same Frame, etc. Have also modified some of the settings in the config.xml file in the app but without success so far. Any assistance would be appreciated. I'm on a chat with Adobe as I'm writing this and they are researching the matter.
Can you post a screenshot of what is happening? Also, please update the thread with Adobe's response when you get it. It would avoid work for the community if Adobe already helped you out.
Apologies for not responding sooner. This is indeed a flaw in the process--there being no immediate navigation back to the App. There may be a workaround, likely a PhoneGap plugin.