In a medium saucepan, combine cranberries, cognac, sugar, and orange juice. Place allspice, cloves, peppercorns, red-pepper flakes, and cinnamon stick in a double layer of cheesecloth; bundle it up, tie with kitchen string, and add to saucepan.
Bring mixture to a boil. Reduce heat to a simmer, and cook, stirring often, until syrupy, 15 to 20 minutes. Discard bundle, and transfer mixture to a bowl, let cool, and refrigerate until needed.