Combine the pomegranate seeds, 1/4 cup pomegranate juice, 1/4 cup apple cider, 1/2 cup sugar, and cinnamon stick in a small saucepan and bring to a boil. Reduce heat to low and simmer for 30 minutes.
In a large saucepan, combine the cranberries, 1/2 cup apple cider, brown sugar, orange juice, bourbon, and orange zest. Cook on medium-high for 10 to 15 minutes, until the liquid has reduced and the cranberries have popped.
Turn off the heat and strain the pomegranate sauce in the small saucepan into the cranberry sauce and stir until incorporated.
Cook on low for 2 to 3 minutes. Remove from the heat and let the cranberry sauce cool for 15 minutes before pouring into mason jars. Let cool to room temperature before sealing and storing in the fridge or freezer.