Line a cookie sheet with parchment paper, or spray with nonstick spray.
In a small bowl, whisk together the coconut sugar, stevia, water, and vanilla until the sugar dissolves.
Add the pumpkin seed butter, flax, flour, and salt and mix well to form a very thick and sticky dough. Stir in the chips.
Using a heaping teaspoon, scoop the dough and roll it into small balls, placing them about one inch apart on the cookie sheet. Flatten slightly with your palm (or use a silicone spatula).
Bake for 10 to 12 minutes, rotating the sheet about halfway through, until the cookies are light golden brown (the dough will lighten as the cookies bake). Allow the cookies to cool completely before removing from the cookie sheet.
Store in an airtight container in the refrigerator for up to 5 days. It may also be frozen.