Is there a good way to set up a pdf document containing hyperlinks before uploading?

Before uploading on Flipsnack our pdf documents are created through Adobe InDesign and hyperlinked through there first. I have noticed that Flipsnack only auto-reads hyperlinks that directly say ".com" on it and not words that are hyperlinked. For example "www.flipsnack.com" vs "Flipsnack" (with the second form being hyperlinked to the url). Is there a workaround to get a better read on it? Thanks!