Yeah, that Search field is kinda clunky. I think it mostly searches our site, but Google inserts some of its own paid ads in there…?
Here’s my little InDesignSecrets secret: The way I search our site normally is to go to google and search for: searchterm site:indesignsecrets.com
When you add that site tag, it limits the search to just our site. :-)
Fortunately, we’re doing a massive site redesign that we hope to roll out next month, and the search is much, much better there.

I suggest contacting the people at Indiscripts and see if you can see why it is not working.

Did you try importing the Acrobat changes with File > Import PDF Comments?
Or are you saying that he actually edited the text inside the PDF file? That would be bad.
When you see the blank pages, did you look inside Edit > Edit with Story Editor? That would tell you if the text is really there, but not showing up.

Acrobat looks for text that looks like a hyperlink and turns them into hyperlinks automatically.

That does seem strange. But in general, it would be far better to apply a different paragraph style to the non-indented paragraphs. (Make one in Word that is based on the main style, but with no first line indent.)