Classical communication systems fail not only through random noise but also when transmitter and receiver use incompatible operational codebooks. Variational autoencoders (VAEs) train an encoder $q_φ$ and decoder $p_θ$ jointly, and practitioners treat the resulting latent space as a discrete code -- for clustering, conditional generation, and mechanistic interpretability. Yet standard VAE diagnostics -- ELBO, active units, mutual information, and code histograms -- certify only whether this code is used, never whether the decoder reads each latent under the encoder's code. We close this gap with the neural codebook channel $K_{e\to d}(j\mid i)$, a coupled encoder-decoder diagnostic whose off-diagonal mass is bounded by an architecture-free Bernoulli-KL certificate $d_{\mathrm{bin}}(1-\mathcal{A} \,\|\, \barη_p) \le \barΔ$ controlled by the variational gap. The certificate is the operational specialization of the classical KL chain rule under disintegration to the encoder-decoder disagreement event, complemented by a constructive marginal-impossibility result: no combination of marginal histograms, entropies, active-code counts, or mutual information determines $K_{e\to d}$. We audit the certificate on four sklearn datasets (finite-grid exact, 5/5 seeds, 20/20 pairs satisfy the bound), a 2D model where the bound is non-vacuous at $2.71\times$ the observed disagreement and the four-term identity closes within $10^{-4}$, MNIST under importance-sampling control, and a VQ-VAE attaining the predicted limit $\hat{\mathcal{A}}=1.000$. The package $(K_{e\to d}, \mathcal{A}, R_{\mathrm{eff}}, R, \mathrm{AU})$ is an audit-ready reporting unit. More broadly, the framework makes mismatched decoding -- a failure mode classical communication theory named decades ago -- visible inside a single deep generative model.