Transparent surfaces, such as glass, create complex reflections that obscure images, posing challenges for various computer vision applications. We present Flash-Split, a robust, two-stage flash-based approach for separating transmitted and reflected light using a single pair of flash/no-flash images, even if they are misaligned. Stage 1 performs separation in latent space via a dual-branch diffusion model, reducing the need for alignment by encoding both transmission and reflection with cross-attention. Stage 2 enhances image sharpness through conditional decoding, blending separated low-frequency and original high-frequency information. Flash-Split achieves state-of-the-art results in single-view reflection separation, validated on synthetic and real-world data, and outperforms existing methods in challenging scenarios.