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Whisk together all-purpose flour, rye flour, cocoa, baking powder, baking soda, and fine sea salt in a medium bowl, and set aside. Whisk together melted vegan butter, cane sugar, brown sugar, and 1/4 cup water in a large bowl. Add flour mixture, and stir until well combined. Stir in bittersweet chocolate until well combined. Cover and chill dough at least 2 hours or up to 3 days.
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Preheat oven to 350°F. Line 3 baking sheets with parchment paper. Using a 2-tablespoon (1 3/4-inch) cookie scoop, drop dough balls (about 1 1/2 ounces each) 2 inches apart onto prepared baking sheets. (Do not flatten.) Sprinkle evenly with flaky sea salt.
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Bake cookies on middle rack of preheated oven, 1 or 2 baking sheets at a time, until set and slightly puffed, 12 to 14 minutes. Let cookies cool on baking sheets 5 minutes; transfer to a wire rack. Repeat with remaining cookies. Serve warm, or let cool completely, about 30 minutes.
Note
If using unsalted butter, increase salt by 1/4 teaspoon per 1/2 cup butter.
Make Ahead
Cookies can be stored in an airtight container at room temperature up to 5 days or frozen up to 1 month.
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