The VS2005 Migration Wizard doesn't seem to handle migrating user controls that have base classes defined in a separate assembly very well. The way to get this to work is
to goto the source view on the user control and set the Inherits page attribute equal to namespace.classname of the assembly that contains the definition.
For example:
Assembly Name: BaseControls
Namespace: BaseControls
ClassName: UserControlBase
You would setup your page attribute in your user control to be:
<% @Control Language="C#" CompileWith="NewUserControl.ascx.cs" ClassName="NewUserControl_ascx" Inherits="BaseControls.UserControlBase" %>
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