Response.Redirect redirects the browser and your javascript is not executing.
Try redirecting in JavaScript:
protected void Page_Load(object sender, EventArgs e)
{
if (Request.QueryString["timeout"] != null && Request.QueryString["timeout"].ToString().Equals("yes"))
{
Response.Write("<script>" +
"alert('Your Session has Timedout due to Inactivity');" +
"location.href='Default.aspx';" +
"</script>");
}
}
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