I have been using LINQ to SQL for a while, and there is one thing that has always bothered me. Whenever I modify the schema of a table, in order to refresh it in the designer, I
Edit the .dbml file that the designer uses to draw the tables and generate the code. I've used this approach when the changes are small (adding a couple of columns, creating a simple table)
Use sqlmetal to create the required xml for the changed tables and move the declarations by hand to the .dbml file. This one is better for when the changes are either more complex or larger.