Place the coconut flakes and water in the container of a high-speed blender, such as Vitamix. Cap it tightly and blend on high speed for 45-60 seconds, until the mixture is smooth and uniformly white. Alternatively, you can use a nut milk machine.
Fit your nut milk bag into a strainer over a medium glass bowl and pour the coconut mixture into the nut milk bag. Allow the liquid to drain into the bowl and gently squeeze the pulp to extract most of the liquid. Discard the coconut pulp and save the liquid for making the yogurt.
Stir the honey into the coconut milk and if you are using tapioca starch as your thickener you can add it now. Heat the mixture to 190 °F in the microwave or a pot over the stove. Once it reaches 190 °F place the milk in the freezer to cool down to 100 °F while you prepare the heat source.
If you are using a sous vide stick, clip it to a large stock pot and add tap water to the minimum water level indicator on the stick. Set the unit to preheat to 98 °F, and set the timer for 12.5 hours (to include heat-up time). Sterilize your jars.
If you are using an Instant Pot, add about two inches of tap water to the pot. Set the timer for 12.5 hours (to include heat-up time). Sterilize your jars.
If you are using a yogurt maker, sterilize the glass container and follow the instructions for preparing your yogurt maker.
Once the coconut milk has cooled to 100 °F, put about ½ cup of the milk into each of the two-quart mason jars (or the yogurt machine container). Add your chosen yogurt starter (probiotic capsule, prepared yogurt, or freeze-dried starter) to the coconut milk in each jar and stir with a non-reactive spoon (wooden or silicone) to combine. Then divide the remaining coconut milk between the jars and give it another stir.
Loosely cap the jars with the mason jar lids, plastic wrap, or the lid from your yogurt maker. Follow the instructions that come with your yogurt maker for what to do next, and set the timer for 12 hours.
If you are using an Instant Pot, gently place the uncovered jars into the Instant Pot so you don't get water from the pot into the jars. Loosely cap the jars. Place the cover on the Instant Pot, press the "Yogurt" button, and adjust the time with the "+" or "-" buttons until you reach 12 hours.
Once the 12 hours is up, remove the yogurt from the yogurt maker / InstantPot / sous vide bath. Dry the jars and then pour all of the yogurt into a blender along with the gelatin. Blend for about 30 seconds, then pour the yogurt back into the jars. Loosely cap the jars again and place the yogurt in the refrigerator to cool and thicken for several hours.
There may be some separation of the liquid and yogurt as it chills. You can simply mix it back together with a spoon. Serve within five days or freeze immediately.