You cannot mix models first and db-first. After you manually modify the database, you will no longer be able to use database generation from EDMX or delete your changes made directly to the database.
In some cases, this can be avoided by downloading the Entity Designer Database Generation Power Pack extension in Visual Studio 2010. When using this extension with VS 2010 Premium or Ultimate, you can use additional DB generation workflows and T4 templates that VS tools can use to comparing a newly created database with an existing database and creating only ALTER scripts.
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