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When you use the update-edmx feature of visual studio.
Your EDMX schema is merged against a database.
UPDATE: looks like new db fields are added to your edmx, modified fields are merged in someway and deleted ones are left in your schema.
TheRules
Added Notes
If any objects have been added to the database (or were not included in the previous storage model), you can add them to the conceptual model -selecting them from the
addtab in the update-edmx window.Updated Nodes
Any changes that have been made to these database objects will be reflected in the updated storage model. Changes to the conceptual model are made when columns are added to a table or view.
Deleted Nodes
If an object has been deleted from the database and was included in the previous storage model. The objects in these nodes will be deleted from the updated model.
via MSDN