Never mind. I re-enabled IIS Express Authentication and my settings were still there. You might want to add this to the SQL migration document as a post installation task.
http://www.lansweeper.com/kb/73/moving-your-database-from-sql-compact-to-sql-server.html
http://www.lansweeper.com/kb/30/How-to-enable-authentication-for-IIS-Express..html