In a high sided sauce pan combine the apple cider, vanilla bean seeds and reserved vanilla bean pod, cinnamon stick, nutmeg and bring to a boil.
Lower to a simmer until reduced to about between ¾ and ⅔ cup. It should be syrupy. When it is getting close to being reduced you can pour into a glass measuring cup to check amount then back into the pan. Once it is between ⅔ and ¾ cup then move on to the next step. This will take about 20 minutes. Remove the cinnamon stick and vanilla bean but leave syrup in pan.
Add in the granulated sugar, brown sugar and salt, stir until dissolved then clip on a candy thermometer and cook without stirring until it reaches 240 deg F. Around 7-8 minutes.
While still on the heat, add in the butter one tablespoon at a time and stir until melted.
Remove pan from the heat and add in the heavy cream and bourbon, being careful as the mixture may bubble up. Heat on low again and stir until it starts to slightly thicken back up, about 1 minute. Bourbon is optional, you can leave out.
Let cool in the pan 10 min while off the heat and then transfer to a glass jar, such as a mason jar, and cool completely. It will firm up as it cools.
Keep refrigerated up to 3 weeks in an airtight container. Up to 2 months frozen. The caramel will firm up in the refrigerator, solidify in the freezer. You can microwave it at 20 seconds at a time to return to a pourable state.