Preheat your oven to 400°F (200°C). Line a baking sheet with parchment paper.
Toss the halved jalapeños with olive oil and kosher salt until evenly coated.
Arrange the peppers cut-side up on the prepared baking sheet.
Roast for 8–10 minutes until the peppers are tender while still holding their shape.
Fill each pepper generously with diced brie cheese.
Return to the oven and bake for another 5–7 minutes, or until the cheese is completely melted and bubbly.
Meanwhile, combine 3/4 cup blueberries, sugar, and lemon juice in a small saucepan over medium heat.
Cook for 8–10 minutes, stirring occasionally and gently crushing some berries until the mixture thickens into a glossy sauce.
Remove from the heat and stir in the remaining blueberries to keep some fresh texture.
Spoon the blueberry mixture over each Blueberry Brie Jalapeño Poppers, allowing some of the sauce to cascade down the sides.
Finish with fresh thyme leaves and black pepper flakes before serving immediately.