Whenever you submit a form to download a file the response sent back is a file. In this case the setter called after the method which does the download has no effect.

 if(form.getDownloadForm != null && form.getDownloadForm.equals("Y"))
 {
   downloadForm(form, request);

   //The Below Setter has No Effect
   form.setDownloadForm("Y");
 }

 class RegisterForm()
 {
   public String downloadForm;

    public void setDownloadForm(String p_download) 
    {
	  this.downloadForm= p_download;
    }
    
    public String getDownloadForm() 
    {
	  return downloadForm;
    }
 } 

The Setter had no effect since the request sent to the downloadForm(form, request); will end up with response of file download and not response which has new values to form set by setter(in our case downloadForm(form, request)) and Page reload.

There are 2 simple fix for this.

Fix 1
One simple fix is to set form hidden property in java script to N after the form get submitted. Note though the form is submitted it is not reloaded with new response since the response sent back is a file.

The Page will be reloaded only when response is sent back to the same URL of browser. Not to the browser as file.

 function downloadWFSetup(pWaterfallId) 
 {	
    $('#downloadForm').val('Y');
    document.WaterfallTriggerForm.submit();

    //This part of code runs even after the form submission since the 
    //response sent is file which does not require page reload
    $('#downloadForm').val('N');			
 }

In our case the page is not going to get reloaded so the java script continues its execution even after form submission setting property of downloadForm to N.

Fix 2
The Other way is to send request in Link with downloadForm=Y. In this case there is no need to to reset the form values as we get the values by request.getParameter() Method.