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In many deployed systems, new text inputs are handled by retrieving similar past cases, for example when routing and responding to citizen messages in digital governance platforms. When these systems fail, the problem is often not the language model itself, but that the nearest neighbors in the embedding space correspond to the wrong cases. Modern machine learning systems increasingly rely on fixed, high-dimensional embeddings produced by large pretrained models and sentence encoders. In real-world deployments, labels are scarce, domains shift over time, and retraining the base encoder is expensive or infeasible. As a result, downstream performance depends heavily on embedding geometry. Yet raw embeddings are often poorly aligned with the local neighborhood structure required by nearest-neighbor retrieval, similarity search, and lightweight classifiers that operate directly on embeddings. We propose PEARL (Prototype-Enhanced Aligned Representation Learning), a label-efficient approach that uses limited supervision to softly align embeddings toward class prototypes. The method reshapes local neighborhood geometry while preserving dimensionality and avoiding aggressive projection or collapse. Its aim is to bridge the gap between purely unsupervised post-processing, which offers limited and inconsistent gains, and fully supervised projections that require substantial labeled data. We evaluate PEARL under controlled label regimes ranging from extreme label scarcity to higher-label settings. In the label-scarce condition, PEARL substantially improves local neighborhood quality, yielding 25.7% gains over raw embeddings and more than 21.1% gains relative to strong unsupervised post-processing, precisely in the regime where similarity-based systems are most brittle.