Set oven to 400°F (205°C). Combine the seeded, halved jalapeño peppers with olive oil and kosher salt. Place them cut-side up on a baking sheet lined with parchment. Roast for 8–10 minutes, until tender and bright green.
Take peppers out of oven and fill each cavity completely with diced brie. Put back in oven for 5–7 minutes, until cheese is bubbly, melted, and gooey white.
In a small saucepan over medium heat, mix 3/4 cup blueberries, sugar, and lemon juice. Simmer for 8–10 minutes, mashing lightly, until a thick, dark purple sweet glaze forms.
Take glaze off heat and fold in remaining 1/4 cup whole blueberries until they blister from residual heat. Spoon mixture over the bubbly brie, letting it drip slightly down the pepper sides. Top with fresh thyme leaves and black pepper flakes. Serve immediately.