Preheat oven to 350º.
Line two large baking sheets with parchment paper.
Using a hand mixer, put butter and shortening in a large mixing bowl and cream together.
Add coconut sugar and honey and mix once more.
Add the eggs, baking soda, and vanilla and mix on high until ingredients are combined well and smooth.
Carefully add tapioca flour a little at a time and mix as you go, then add coconut flour and finish combining with the hand mixer on high.
Add the chocolate chips and optional pecans and mix once more until distributed.
Let the dough rest for about 15 minutes.
Place tablespoon-sized balls of dough about two inches apart on the cookie sheets. I like to only bake one sheet at a time because the bottom rack always cooks a little differently, so I could in two batches.
Bake for approximately 10-12 minutes (ovens vary). They will begin to brown on the edges when they are done.
When you remove them from the oven, they will be a bit crumbly. Let them sit on the cookie sheet undisturbed for about ten minutes before transferring to a cooling rack, otherwise they will not hold up as well.