Peel the quinces, remove the cores and cut into cubes. Heat the butter over low heat in a saucepan and fry the shallots. Then add the quince and fry for about 5 minutes. Deglaze with the apple cider vinegar and then add the sugar. Simmer gently for about an hour until the quince is soft and the sugar has thickened.
Preheat the oven to 200°C. Cut the filo pastry sheets into quarters and brush all the sheets on both sides with the melted butter. Also grease the cupcake tray with the melted butter. Place a sheet of phyllo dough in one of the cups and place the next sheet diagonally. Push them in gently to form cups.
Bake the phyllo dough cups for about 5 minutes in the oven until they are almost done. Then take them out and divide the goat cheese, quince chutney and pistachios over the cups and put them back in the oven until the phyllo dough cups are golden brown and crispy.
Save the leftover quince chutney for another recipe.