Fill two 9x13-inch baking dishes with 1-inch of water each. Place three acorn squash halves cut-side-down into each baking dish. Bake in the preheated oven until the squash is very tender and the skin begins to separate from the meat, about 1 hour. Remove, discard the water, and set aside until cool enough to handle.
Scoop the acorn squash flesh from the skins and into a blender. Add the cinnamon, nutmeg, ginger, and cloves. Puree until thick and smooth. Scrape the squash into a heavy-bottom pot, and stir in the brown sugar and apple juice concentrate. Cook and stir over medium-low heat until thickened, 40 to 45 minutes. Cool completely before packing into freezer-safe containers. Store in the freezer up to 6 months.
