Have you tried the latest v3 early access build? This has a feature that lets you add your own custom migration script to override default behavior. What you need to do is to add a migration script to cover the change in which the NOT NULL column was added, and to edit the default script to add the UPDATE statement.
http://www.red-gate.com/MessageBoard/vi ... hp?t=14110
This feature works with TFS, SVN and Vault for the time being. Which do you use?
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