There are three ways to keep the model in sync.
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Delete the modified tables from the designer, and drag them back
onto the designer surface from the Database Explorer. I have found
that, for this to work reliably, you have to:
a. Refresh the database schema in the Database Explorer (right-click, refresh)
b. Save the designer after deleting the tables
c. Save again after dragging the tables back.
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Use SQLMetal to regenerate the schema from your database. I have seen a number of blog posts that show how to script this.
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Make changes directly in the Properties pane of the DBML. This works for simple changes, like allowing nulls on a field.