Fill two 20x30cm baking dishes with 2.5cm 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 flesh, 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-bottomed saucepan, and stir in the dark brown soft sugar and apple juice. 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.