Suppose you have:
var htmlLoader:HTMLLoader = new HTMLLoader();
//Add to display list, load content, etc...
Then you can access the window object of the loaded page
If the HTMLLoader loads a PDF file directly, I suspect that
under the covers AIR embeds it in an HTML page. So you could still
access htmlLoader.window and then find the PDF object in the page.
(I haven't tried this myself, though.)