Remove from heat and pour into a glass bowl (I find a 2 cup measuring cup works best for this). Let cool at room temperature for 30-40 minutes, stirring occasionally. The caramel is ready when it coats the back of a spoon and ribbons as it falls. Don't wait too long or the caramel will become too thick to coat the apples evenly.
Dip the apples into the caramel going 3/4 of the way up. If you find that the caramel is running off the apples too much, leave it to cool longer. You can also place the caramel in the fridge for 15 minutes to help it thicken.
Place the coated apples upright on the prepared baking tray and cool in the fridge for at least 2 hours. Sprinkle with flaked sea salt before serving.
This caramel sauce doesn't set in the same way as conventional caramel; it remains on the softer side. If you can't find brown rice syrup, you can exchange it for maple syrup or agave nectar in equal measure; however, I have found brown rice syrup much easier to work with- it won't crystallize during heating. For my apples, I coated them in a layer of caramel, let them set in the fridge for 10 minutes, and then drizzled any remaining caramel down the sides for a "drippy candle" look.