I have a .Net 2.0 application.  Nightly I, the application would error out and I would get a “Server Error in ‘/’ Application.”

Then it would also say something like…

Could not load file or assembly ‘App_Web_e4mmjsth, Version=0.0.0.0, Culture=neutral, PublicKeyToken=null’ or one of its dependencies. The system cannot find the file specified.

The detail would have something like…

Line 1: <%@ Control Language=”C#” AutoEventWireup=”true” CodeFile=”~/Controls/MyControl.ascx.cs” Inherits=”Controls_MyControl” %>

Basically, after recompiling I guess the .Net application restarts the application.  However it deletes one of the temporary files.

I found a whole thread about it HERE. 

Then found the error…
http://support.microsoft.com/default.aspx?scid=kb;EN-US;934839

Then the download is on…
http://connect.microsoft.com/VisualStudio/content/content.aspx?ContentID=3705
(You have to download the 934839 one)

This should fix the problem.