diff --git a/control-pipeline/services/batch_dedup_runner.py b/control-pipeline/services/batch_dedup_runner.py
index 8dad13c..27564a0 100644
--- a/control-pipeline/services/batch_dedup_runner.py
+++ b/control-pipeline/services/batch_dedup_runner.py
@@ -346,13 +346,40 @@ class BatchDedupRunner:
 
         self._progress_total = total
         self._progress_count = 0
-        logger.info("BatchDedup Cross-group: %d masters to check", total)
         cross_linked = 0
         cross_review = 0
 
-        # Paginated processing — 100 rows per DB query
+        # Checkpoint: resume from last processed control_id
         DB_PAGE = 100
-        last_control_id = ""
+        # Checkpoint: resume from last processed control_id (survives container restart)
+        checkpoint_row = self.db.execute(text("""
+            SELECT config FROM canonical_generation_jobs
+            WHERE status = 'dedup_phase2_checkpoint'
+            LIMIT 1
+        """)).fetchone()
+        last_control_id = checkpoint_row[0] if checkpoint_row else ""
+
+        if last_control_id:
+            skip_row = self.db.execute(text("""
+                SELECT COUNT(*) FROM canonical_controls
+                WHERE decomposition_method = 'pass0b'
+                  AND release_state != 'duplicate'
+                  AND release_state != 'deprecated'
+                  AND control_id <= :last_id
+            """), {"last_id": last_control_id}).fetchone()
+            skipped = skip_row[0] if skip_row else 0
+            self._progress_count = skipped
+            logger.info("BatchDedup Cross-group: RESUMING from %s (skipping %d already processed)",
+                         last_control_id, skipped)
+        else:
+            self.db.execute(text("""
+                INSERT INTO canonical_generation_jobs (id, status, config)
+                VALUES (gen_random_uuid(), 'dedup_phase2_checkpoint', '')
+            """))
+            self.db.commit()
+
+        logger.info("BatchDedup Cross-group: %d masters to check (starting from %s)",
+                     total, last_control_id or "beginning")
 
         while True:
             rows = self.db.execute(text("""
@@ -461,11 +488,34 @@ class BatchDedupRunner:
 
                 self._progress_count += 1
 
-            # Log progress every page
+            # Save checkpoint + log progress every page
+            try:
+                self.db.execute(text("""
+                    UPDATE canonical_generation_jobs
+                    SET config = :cid
+                    WHERE status = 'dedup_phase2_checkpoint'
+                """), {"cid": last_control_id})
+                self.db.commit()
+            except Exception:
+                try:
+                    self.db.rollback()
+                except Exception:
+                    pass
+
             processed = self._progress_count
             if processed % 500 < DB_PAGE:
-                logger.info("BatchDedup Cross-group: %d/%d checked, %d linked, %d review",
-                            processed, len(rows), cross_linked, cross_review)
+                logger.info("BatchDedup Cross-group: %d/%d checked, %d linked, %d review (checkpoint: %s)",
+                            processed, total, cross_linked, cross_review, last_control_id)
+
+        # Clear checkpoint on completion
+        try:
+            self.db.execute(text("""
+                DELETE FROM canonical_generation_jobs
+                WHERE status = 'dedup_phase2_checkpoint'
+            """))
+            self.db.commit()
+        except Exception:
+            pass
 
         self.stats["cross_group_linked"] = cross_linked
         self.stats["cross_group_review"] = cross_review