Line 2 baking sheets with parchment. Place the chocolate-covered espresso beans in the freezer for 10 minutes, then chop with a serrated knife; reserve about 1/3 cup for topping. Preheat the oven to 325°F (165°C) and position racks in the upper- and lower-thirds.
In a medium bowl, whisk together the flour, instant espresso powder, baking soda, salt, and cinnamon until evenly blended.
In a large mixing bowl, beat the softened butter, brown sugar, and granulated sugar on medium speed until light and slightly fluffy, about 2 minutes. Scrape the bowl. Beat in the vanilla and molasses. Add the eggs one at a time, mixing for 30 seconds after each until smooth.
Add the dry ingredients in two additions on low speed, mixing just until a few floury streaks remain. Fold in the chopped espresso beans, reserving the set-aside portion for topping.
Refrigerate the dough for 20 minutes to firm slightly. Meanwhile, clean off the baking area and ready a 2-tablespoon scoop (about 35–40 g dough each).
Scoop dough onto prepared sheets, spacing about 2 inches apart. Lightly press a few of the reserved chopped beans onto the tops and gently flatten each mound to roughly 3/4-inch thick.
Bake 12–14 minutes, rotating and switching pans halfway through, until edges are set and centers look soft and slightly underdone. If baking one sheet at a time, keep remaining dough chilled between batches.
Cool on the pan for 5 minutes, sprinkle with flaky sea salt if using, then transfer to a wire rack to cool completely.