Hello Chinmaya,
Thank you for posting this question. It
looks like this is not directly supported by HTML2PDF at this time. All links created by HTML2PDF go through the web browser.
However, it is possible to
modify the PDF in question to launch in a PDF viewer instead of through
the browser. At issue is the "Action" associated with each
link annotation. Actions are used to determine how a link should
be handled by a PDF viewer. HTML2PDF inserts "URI" actions, which
tell the viewer to go through a web browser. What you want are "Launch" actions, which
tell the viewer to launch files based on however the operating system launches that file
type.
The annotation sample at
http://www.pdftron.com/pdfnet/samplecode.html#Annotation
shows how to loop over all the annotations of a PDF document. It shows
how to find all Link annotations with URI actions. You would want to
get the existing URI string for each annotation's action, as the sample shows,
and to strip out any unwanted information from that string (such as the
"file:///"). Then use Action.CreateLaunch to create a new action with the file name, and Link.SetAction to associate it with the link annotation.
Please let us know if you run into any problems.