Make sure you give an ID to the <link> element that contains the StyleSheet, like:
<link id="masterStyle" href="MasterStyleSheet.css" type="text/css" rel="stylesheet" runat="server" />
Then in the codebehind (PageLoad) you can add the following code to replace the MasterPage stylesheet:
// Add additional StyleSheet(s)
HtmlLink stylesheetControl = (HtmlLink)Page.Master.FindControl("masterStyle");
if (stylesheetControl != null)
{
stylesheetControl.Href= @"<link href=""NewStyleSheet.css"" type=""text/css"" rel=""stylesheet"" />";
}
PS: Just to make sure, use:
using System.Web.UI.HtmlControls
in both my examples :)