diff --git a/control-pipeline/api/control_generator_routes.py b/control-pipeline/api/control_generator_routes.py
index dd05be0..37b9ae8 100644
--- a/control-pipeline/api/control_generator_routes.py
+++ b/control-pipeline/api/control_generator_routes.py
@@ -1999,20 +1999,14 @@ async def _run_harmonization_recheck(req: HarmonizationRecheckRequest, job_id: s
         """), {"since": req.since, "until": req.until}).fetchall()
 
         target_ids = {r[0] for r in targets}
-
-        # Load ALL other draft controls (the reference set)
-        all_drafts = db.execute(text("""
-            SELECT id::text, control_id, title, objective
-            FROM compliance.canonical_controls
-            WHERE release_state = 'draft'
-            ORDER BY control_id
-        """)).fetchall()
-
-        # Exclude targets from reference set
-        reference = [r for r in all_drafts if r[0] not in target_ids]
-
         total_targets = len(targets)
-        total_reference = len(reference)
+
+        # Count reference controls (all drafts except targets)
+        total_reference = db.execute(text("""
+            SELECT COUNT(*) FROM compliance.canonical_controls
+            WHERE release_state = 'draft'
+              AND NOT (updated_at >= CAST(:since AS timestamp) AND updated_at < CAST(:until AS timestamp))
+        """), {"since": req.since, "until": req.until}).scalar()
 
         _harmonization_recheck_status[job_id] = {
             "status": "phase1_indexing", "total_targets": total_targets,
@@ -2037,40 +2031,60 @@ async def _run_harmonization_recheck(req: HarmonizationRecheckRequest, job_id: s
                 "vectors": {"size": dim, "distance": "Cosine"},
             })
 
-        # Index reference controls in batches
-        BATCH = 32
+        # Index reference controls in paginated batches (never load all into memory)
+        EMBED_BATCH = 8
+        DB_PAGE = 500
         indexed = 0
-        for i in range(0, total_reference, BATCH):
-            batch = reference[i:i + BATCH]
-            texts = [f"{r[2] or ''} {(r[3] or '')[:200]}" for r in batch]
+        db_offset = 0
 
-            async with httpx.AsyncClient(timeout=60.0) as client:
-                resp = await client.post(f"{EMBEDDING_URL}/embed", json={"texts": texts})
-                if resp.status_code != 200:
-                    continue
-                embeddings = resp.json().get("embeddings", [])
+        while db_offset < total_reference + DB_PAGE:
+            page_rows = db.execute(text("""
+                SELECT id::text, control_id, title, objective
+                FROM compliance.canonical_controls
+                WHERE release_state = 'draft'
+                  AND NOT (updated_at >= CAST(:since AS timestamp) AND updated_at < CAST(:until AS timestamp))
+                ORDER BY control_id
+                LIMIT :lim OFFSET :off
+            """), {"since": req.since, "until": req.until, "lim": DB_PAGE, "off": db_offset}).fetchall()
 
-                points = []
-                for j, (r, emb) in enumerate(zip(batch, embeddings)):
-                    if not emb:
-                        continue
-                    points.append({
-                        "id": str(_uuid.uuid5(_uuid.NAMESPACE_DNS, r[0])),
-                        "vector": emb,
-                        "payload": {"control_uuid": r[0], "control_id": r[1], "title": r[2] or ""},
-                    })
+            if not page_rows:
+                break
 
-                if points:
-                    await client.put(
-                        f"{QDRANT_URL}/collections/{RECHECK_COLLECTION}/points",
-                        json={"points": points},
-                    )
-                    indexed += len(points)
+            for eb_start in range(0, len(page_rows), EMBED_BATCH):
+                batch = page_rows[eb_start:eb_start + EMBED_BATCH]
+                texts = [f"{r[2] or ''} {(r[3] or '')[:200]}" for r in batch]
 
-            if (i + BATCH) % 1000 < BATCH:
-                _harmonization_recheck_status[job_id]["indexed"] = indexed
-                _harmonization_recheck_status[job_id]["status"] = "phase1_indexing"
-                logger.info("Recheck indexing: %d/%d reference controls", indexed, total_reference)
+                try:
+                    async with httpx.AsyncClient(timeout=30.0) as client:
+                        resp = await client.post(f"{EMBEDDING_URL}/embed", json={"texts": texts})
+                        if resp.status_code != 200:
+                            continue
+                        embeddings = resp.json().get("embeddings", [])
+
+                        points = []
+                        for r, emb in zip(batch, embeddings):
+                            if not emb:
+                                continue
+                            points.append({
+                                "id": str(_uuid.uuid5(_uuid.NAMESPACE_DNS, r[0])),
+                                "vector": emb,
+                                "payload": {"control_uuid": r[0], "control_id": r[1], "title": r[2] or ""},
+                            })
+
+                        if points:
+                            await client.put(
+                                f"{QDRANT_URL}/collections/{RECHECK_COLLECTION}/points",
+                                json={"points": points},
+                            )
+                            indexed += len(points)
+                except Exception as e:
+                    logger.warning("Indexing batch error at offset %d: %s", db_offset + eb_start, e)
+
+            db_offset += DB_PAGE
+            _harmonization_recheck_status[job_id]["indexed"] = indexed
+            _harmonization_recheck_status[job_id]["status"] = "phase1_indexing"
+            if db_offset % 5000 < DB_PAGE:
+                logger.info("Recheck indexing: %d/%d", indexed, total_reference)
 
         logger.info("Recheck Phase 1 done: %d reference controls indexed", indexed)