Preheat the oven to 350 degrees Fahrenheit.
Prepare a 9-inch square baking pan by spraying the bottom and sides with cooking spray, then line with parchment paper to cover the bottom and the sides. Spray cooking spray over the parchment. You should leave an overhang so you can lift the brownie out after it bakes. If using a round tin, you can use a springform pan, and line the bottom with parchment.
Place the cherries in a small saucepan with the sugar. Cook, stirring occasionally, until all of the cherries have released their juices. Continue cooking another 10 minutes or so until most of the juice has evaporated. Turn off the heat. You should have just over half a cup of cooked cherries including juices.
Place the almond flour in a bowl, add the cocoa, tapioca flour, baking powder and baking soda, and mix well. Add the cooked cherries, maple syrup, vanilla extract, almond milk, apple cider vinegar and salt to the bowl and mix it all well. Stir in the chocolate chips. You will have a thick batter but you should be able to pour it into the baking pan and smooth it with a spatula.
Bake 35 minutes or until a toothpick in the center comes out clean.
Cool on a rack 30 minutes, then slide a knife along the edges to release. Lift the brownie out of the pan. Let it cool thoroughly before cutting into individual pieces and serving.