Ghost Vectors: Soft-Deleted Embeddings Remain Reconstructible in HNSW Vector Databases

Abstract: Retrieval-augmented generation (RAG) allows LLMs to access external and private corpora for factual, domain-specific responses. Modern RAG pipelines use hierarchical navigable small world (HNSW) vector databases for efficient similarity search. When a user requests data deletion, the systems typically only mark the record as deleted, leaving the embedding on disk physically unchanged. This soft-delete operation raises compliance concerns under data-erasure and retention requirements such as GDPR Article 17 and HIPAA. Analysis on three HNSW implementations confirms that deleted vectors remain physically recoverable by accessing the raw index files at the storage layer, bypassing API access. Using the Vec2Text inversion model without domain-specific fine-tuning, we show this vulnerability on multiple real-world datasets and data modalities. On Wikipedia biographical living persons dataset (BLP), we successfully recover 25.5% of exact person names and 46.4% of geographic locations (ROUGE-L 0.185). Recovery reaches 100% for both patient age and gender markers (ROUGE-L 0.290) on highly structured, sensitive data (NIH Synthea dataset). On soft-deleted image embeddings, we show 100% tissue classification on histopathology patches (p=1.02e-07) and top-1 identity recovery reaches 99% on facial embeddings (p<0.01). This work introduces Epoch Key Rotation, which encrypts vectors and discards the key upon deletion. Epoch key rotation reduces observed PII recovery to 0% and completes in 2.5 ms for 500 deleted vectors (approximately 0.005 ms/record). Additionally, it generates an ECDSA-signed cryptographic proof as an auditable record of the deletion event.