diff --git a/compliance-agent/src/pipeline/orchestrator.rs b/compliance-agent/src/pipeline/orchestrator.rs
index da92ade..8f038ea 100644
--- a/compliance-agent/src/pipeline/orchestrator.rs
+++ b/compliance-agent/src/pipeline/orchestrator.rs
@@ -277,8 +277,10 @@ impl PipelineOrchestrator {
             }
         }
 
-        // Dedup against existing findings and insert new ones
+        // Dedup against existing findings: insert first-seen ones, and refresh the
+        // control mappings on ones we've seen before.
         let mut new_count = 0u32;
+        let mut refreshed_count = 0u32;
         let mut new_findings: Vec<Finding> = Vec::new();
         for mut finding in all_findings {
             finding.scan_run_id = Some(scan_run_id.to_string());
@@ -293,8 +295,25 @@ impl PipelineOrchestrator {
                 finding.id = result.inserted_id.as_object_id();
                 new_findings.push(finding);
                 new_count += 1;
+            } else if !finding.control_refs.is_empty() {
+                // Re-scan refresh: a mapping pass (newly enabled or tuned) computed
+                // control_refs for a finding first seen before mapping ran. Persist
+                // them onto the existing row — the insert path alone never would.
+                self.db
+                    .findings()
+                    .update_one(
+                        doc! { "fingerprint": &finding.fingerprint },
+                        doc! { "$set": { "control_refs": finding.control_refs.clone() } },
+                    )
+                    .await?;
+                refreshed_count += 1;
             }
         }
+        if refreshed_count > 0 {
+            tracing::info!(
+                "[{repo_id}] Refreshed control_refs on {refreshed_count} existing findings"
+            );
+        }
 
         // Remove stale SBOM entries for this repo before reinserting
         if !sbom_entries.is_empty() {