Many thanks for your post.
Unfortunately SQL Refactor doesn't support dynamic sql. SQL Refactor uses the SQL Compare engine to build up a dependency ordered schema representation to then create the change script.
I have spoken to the SQL Compare developers and,logged it as a feature request in our internal tracking system whose tracking id is SR-895
However, I have added your comments to a feature request ticket for adding dynamic sql support.
The more people that request this the more likely it is to be supported in the future.
Kindly let us know if you have any issues or questions regarding the product,I'll like to help.