Add the Almond milk and apple cider vinegar together in a small bowl, stirring together until combined and letting it sit for 5 minutes until it becomes "slightly thickened" and activated.
Preheat your oven to 375F. Lightly grease your muffin pan (for larger muffins) or for standard muffins, line the wells with liners.
In a large bowl, add the flour, baking powder, baking soda, sugar, cinnamon, nutmeg, and sea salt and mix together until combined. Add in the milk-ACV mixture, melted butter, vanilla, and Agave, mixing together until combined. NOTE: DO NOT OVER-MIX!
Fold in the fresh blueberries and blackberries.
NOTE: The batter should look moist, but thick where it's 'scoop-able' but not easily poured. If way too thick, add 1-2 Tbsps more milk. If too runny, add more flour, 1 Tbsp at a time.
In the prepared muffin pan, add 1 Tbsp of batter to fill each muffin cavity half way. Then, add 1 Tbsp of blueberry preserves into each cavity atop batter followed by another Tbsp of batter to cover the preserves.
Now, add additional blueberries/blackberries atop the batter (gently pressing them in) if desired and place it in the oven.
Bake muffins for 20 to 24 minutes or until the centers come out clean. Once fully baked through, remove from oven and let the muffins cool in the pan before removing.