In a medium saucepan combine 2 cups of the blueberries, brown sugar, vinegar, lemon juice, kosher salt, and black pepper. Bring to boiling, stirring to dissolve sugar. Reduce heat; simmer, uncovered, about 20 minutes or until slightly thickened, stirring occasionally. Remove from heat; cool slightly.
Use immersion blender or transfer to a blender to puree blueberry mixture until smooth. Let cool (mixture will thicken). Stir in remaining blueberries and ketchup. Chill for up to 2 weeks.