In aspx page when you have something like this with ID and runat="server" tags then you change set the attribute for href directly in server side.
<%@ Page Language="C#" AutoEventWireup="true" CodeFile="Default.aspx.cs" Inherits="_Default" Title="title" %>
<link href="~/Styles/Default.css" rel="stylesheet" type="text/css" id="stylesheet" runat="server" />
In server side you call add the code
protected void Page_Load(object sender, EventArgs e)
{
stylesheet.Attributes["href"] = "Newstyle.css";
}
If you are wanting to edit the css file at run time refer this link
http://stackoverflow.com/questions/1637934/is-it-possible-to-edit-or-modify-css-file-at-run-time[
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