I have a PDF file embedded with the page and I have a download link which is used to download that pdf file. When I click on the download link, it will not work since it is the same url as with the embedded pdf; and because the adobe reader is already loaded in the browser it will automatically opens in a new window and the embedded pdf will be unloaded.

To prevent this scenario, we can use the following mechanism. First create a hidded iFrame in the same window using the following code.

<iframe style="DISPLAY: none" src="/" name="iframe1"></iframe>;

Now make a small change to your download link so that the url target is pointing to the hidden frame as shown below..

<a href="http://www.yoursite.com/..." target="iframe1">Download</a>

This will solve the problem. However this method has not been tested with the browsers other than Internet Explorer, Firefox and Netscape.