Preheat oven to 350°F (177°C). Line 2 cupcake tins with paper liners and set aside.
In a large mixing bowl or stand mixer with the paddle attachment, beat butter, vanilla, sugar, and lemon zest on medium speed until light and fluffy (about 2 minutes).
Add eggs one at a time, mixing well after each addition.
Reduce mixer speed to low and beat in sour cream, followed by milk. Turn mixer off.
Add 3¼ cups cake flour, baking powder, baking soda, and salt. Toss the dry ingredients gently with a fork before folding them into the wet mixture. Mix with a spatula until just combined—do not overmix.
In a separate small bowl, toss blueberries with the remaining 2 tbsp of cake flour, then gently fold them into the batter.
Divide batter evenly among cupcake liners, filling each about ¾ full.
Bake one tray at a time for 18–21 minutes, or until a toothpick inserted in the center comes out clean.
Let cupcakes cool completely on a wire rack before frosting.