Preheat the oven to 350°F and line two cookie sheets with parchment paper or silicone baking mats. Also, combine the ground flaxseed and water in a small bowl and mix until well combined. Set aside for 5 to 10 minutes to gel.
In a mixing bowl or stand mixer, whisk the butter and brown sugar until it is creamed together, about 4 to 5 minutes. Then add in the flax eggs, plant-based milk, and vanilla. Mix until combined, about another 2 to 3 minutes.
Next, stop the mixer and add the flour, baking soda, baking powder, and salt. Turn the mixer on low speed, and mix until just combined. If the dough is very dry, you can add another tablespoon or two of plant-based milk to bring the dough together. Just be careful not to add too much, as it will give your cookies a cake-like texture rather than a cookie-like texture.
Add in the dried cherries, pistachios, and dark chocolate, and gently mix to combine and evenly distribute throughout the dough.
Optional: Chill the dough for 30 minutes. This will help prevent the cookies from spreading too much while baking. The cookies are delicious either way!
Using a 1½ tablespoon cookie scoop, scoop a cookie, then place the dough on the prepared baking sheets. Make sure to leave a little room between each cookie, as they will spread while baking. Then, slightly flatten each dough ball so the cookies will bake evenly. If you want to freeze the cookie dough, freeze it after this step.
Bake for 12 to 14 minutes, until the cookies are barely golden around the edges. They will be puffy and lightly colored. They will still be soft when you pull them out of the oven, and the cookies will continue to cook for a few minutes after you remove them from the oven.
Let the cookies cool on the cookie sheet for 3 to 5 minutes, then transfer to a cooling rack for an additional 10 minutes. The cookies will firm up as they cool.
Storage Instructions: Store leftover cookies in an airtight container at room temperature for up to 5 days. To keep them soft, add a small piece of bread or an apple slice to the container. To freeze baked cookies, place them in a single layer on a baking sheet to firm up, then transfer to a freezer-safe bag or container and freeze for up to 3 months. You can also freeze the dough—scoop it into balls, freeze on a tray until solid, and store in a freezer bag for freshly baked cookies anytime.
Reheating Instructions: Warm room-temperature cookies in a 300°F oven for 3 to 4 minutes or microwave for about 10 seconds until soft and melty again. To reheat from frozen, place cookies on a baking sheet and warm in a 300°F oven for 8 to 10 minutes, or let them thaw at room temperature for 20 to 30 minutes before enjoying.