Preheat the oven to 350 degrees F (175 degrees C).
Stir water and flaxseed meal together in a small bowl. Let stand until thickened, about 5 minutes.
Beat butter and both sugars with an electric mixer in a large bowl until creamy. Add eggs, one at a time, beating well after each addition. Add flax mixture and vanilla; mix until well combined.
Stir flour, yeast, baking soda, and salt together in a bowl. Mix dry ingredients into the wet ingredients until well combined. Stir in oats, chocolate chips, and honey. Drop spoonfuls of dough 2 inches apart onto ungreased baking sheets.
Bake in the preheated oven until edges are golden, 12 to 15 minutes.
Remove cookies from the oven and transfer to wire racks to cool.