For the batter and filling: Preheat the oven to 400 degrees F.
In a large bowl, add the cornbread mix. In a medium bowl, whisk the milk, paprika, bacon, eggs, scallions and lime zest. Fold the egg mixture into the cornbread mix. Let rest 5 minutes.
In a 12-cup muffin tin lined with muffin liners, divide half of the batter among all 12 cups. Then add the mozzarella in an even layer and top each with a piece of pepper jack. Gently press down to make everything even. Pour over the remaining batter and spread evenly. Bake until the tops are golden, about 20 minutes.
For the glaze: Meanwhile, in a small pot, add the jelly, lime juice, butter and a splash of water. Heat until the mixture begins to simmer.
Remove the muffins from the oven and immediately pour a spoonful of the glaze over the top of each. Serve warm.