Mix the brown sugar and water in a heavy pan over low heat.
Stir until the sugar has dissolved.
Allow to cool 30 minutes.
Preheat the oven to 250 degrees F.
Strain the jalapeno slices from their liquid. Let sit in a strainer for 15 minutes, shaking every now and then to remove any drained liquid.
Toss the jalapenos in a bowl with just enough simple syrup to coat, 3 to 4 tablespoons.
Arrange on a single layer on a baking sheet.
Bake in the oven for 2 hours, or until crisp, flipping once.
Set aside to cool.
Place back in the original jar with enough simple syrup to cover.
Store in fridge until ready to use.