Please clarify: are these internal links already built into your PDF document, e.g. as internal links to figures and references?
If so, then perhaps pdf2html or another similar tool will create the analogous links within the output HTML. I suggest that you try it.
If not, then please explain how you wish/expect to add these links.
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Another question: is it adequate for the app to be operable when the user is online, or is offline operability a requirement? If the latter, might online-only access be acceptable in the first iteration of your app?