Measure and toast rye flour. Carefully tip flour into a medium skillet and set over medium heat. Stirring frequently, toast 7 minutes, or until flour edges just a couple shades darker and becomes very fragrant. Keep a very close eye during the last 4 minutes. Scrape flour into a mixing bowl, and mix in all-purpose flour, baking soda, and sea salt.

In the bowl of your stand mixer fitted with the paddle attachment or with a hand-held mixer, beat butter on low speed until pale and fluffy, scraping down sides as needed. Add sugar and molasses, and mix 4 minutes more. Add eggs one at a time, scraping down sides as needed. Add vanilla and mix until incorporated. With mixer on low, fold flour mixture in in two batches. Finally, fold in chocolate chips, mixing just until chocolate is well distributed.

With a 1-ounce cookie scoop or using two spoons, measure 3 tablespoons dough into round balls. Arrange 6 - 8 on baking sheet. Sprinkle each ball of dough with a generous pinch of flaky sea salt.