Unfortunately we don't understand your scenario of using a list of downloadable links. Is it a UserControl or you are adding hyper links with RadEditor?
However in case you want to have URL paths resolved on the server in your application, you could use a server link control, e.g.:
<asp:HyperLink ID="link1" runat="server" NavigateUrl="~/files/folder1/apofaseis_ds_2003.zip">Link1</asp:HyperLink>
Please, let us know if we are missing something.
the Telerik team