Melt 40 g butter in a saucepan over medium heat, stir in 2 tablespoons flour, and cook for 1-2 minutes while stirring constantly.
Slowly whisk in 700 ml milk to avoid lumps, then simmer over medium heat for 15-20 minutes, stirring occasionally.
Remove from heat and stir in the grated Emmentaler and Gouda cheese until completely melted and smooth.
Season with salt, pepper, nutmeg, and 2 cl kirsch to taste.
Pour the cheese mixture into oven-safe molds (10 cm diameter, 300 ml capacity each).
Halve the 2 frozen puff pastry sheets and roll out on a floured surface until each piece is approximately 2 cm larger than the mold diameter.
Whisk the egg yolk and brush the pastry pieces with it.
Place each pastry piece coated-side down over a mold, press the overlapping edges down firmly, and brush the top with the remaining egg yolk.
Bake in a preheated oven at 200°C (392°F) regular or 180°C (356°F) convection, on the second rack from the bottom for 15-20 minutes until the pastry is golden brown and puffed.
Serve with canapes or other items for dipping alongside the baked cheese fondue.