In a large saucepan, combine cherry juice and pomegranate juice. Stir in pectin until dissolved. Stir in pepper flakes. Bring to a full rolling boil over high heat, stirring constantly.
Add sugar in a steady stream, stirring constantly to dissolve sugar. Boil hard for 1 minute.
Remove from heat and skim off foam if needed. Stir for 5 to 8 minutes to prevent pepper flakes from floating. (if desired pour mixture through a fine sieve to remove pepper flakes and omit the stirring step).
Ladle into prepared jars leaving a 1/4" headspace. Process jars for 10 minutes in a boiling water bath. Adjust time according to your altitude.
Variations:Hot Cherry - Omit the pomegranate juice and use a total of 4 cups sour cherry juice.
Hot Cherry Cinnamon - Add 1 - 5" stick of cinnamon with the hot pepper flakes. Remove cinnamon stick after skimming, or pour mixture through a sieve to remove pepper flakes and cinnamon. Alternatively, stir in 2 Tbsp cinnamon liqueur after skimming off foam.
Sweet Cherry Pomegranate - Omit the hot pepper flakes.
Hot Cherry Pomegranate Balsamic - Replace 1/4 cup of the cherry or pomegranate juice with balsamic vinegar.