Preheat the oven to 375°F/190°C and line 3 baking sheets with parchment paper. Make sure the oven rack is in the middle of the oven.
Make the flax egg. In a small bowl, mix together the flax seeds and the hot water. Set aside for 5 minutes to gel.
Mix the wet ingredients. In a large mixing bowl with a hand mixer or in a stand mixer with a paddle attachment, cream the vegan butter with the granulated sugar and brown sugar until light and fluffy, about 2 minutes on medium speed. Add the flax egg and vanilla, mixing again for another 30 seconds.
Add the dry ingredients. Turn the mixer off and add into the same bowl the flour, baking soda, baking powder, salt, chocolate chips, and chopped peanut butter cups.
Shape. Use a one tablespoon scoop to make the cookie dough balls. Place 12 to a tray as they do spread a little bit. Press any extra bits of cups or chocolate chips into the tops of the cookies, if desired.
Bake. Bake each cookie tray for 12 to 13 minutes or until the cookies are golden brown. Remove them from the oven and let them cool on the cookie tray for at least 10 minutes before placing them on a wire rack to cool completely.
Cool and enjoy!!