We demonstrate, on a scramjet combustion problem, a constrained probabilistic learning approach that augments physics-based datasets with realizations that adhere to underlying constraints and scatter. The constraints are captured and delineated through diffusion maps, while the scatter is captured and sampled through a projected stochastic differential equation. The objective function and constraints of the optimization problem are then efficiently framed as non-parametric conditional expectations. Different spatial resolutions of a large-eddy simulation filter are used to explore the robustness of the model to the training dataset and to gain insight into the significance of spatial resolution on optimal design.