diff --git a/core/record/record.go b/core/record/record.go
index 4b7fb0a..32938ad 100644
--- a/core/record/record.go
+++ b/core/record/record.go
@@ -237,7 +237,8 @@ func normalizedRefs(in []RelationshipRef) []RelationshipRef {
 			ID:    strings.TrimSpace(in[i].ID),
 			Extra: cloneRawMessages(in[i].Extra),
 		}
-		key := ref.Kind + "\x00" + ref.ID
+		extraKey := rawMapStableKey(ref.Extra)
+		key := ref.Kind + "\x00" + ref.ID + "\x00" + extraKey
 		if _, ok := seen[key]; ok {
 			continue
 		}
@@ -246,6 +247,9 @@ func normalizedRefs(in []RelationshipRef) []RelationshipRef {
 	}
 	sort.SliceStable(refs, func(i, j int) bool {
 		if refs[i].ref.Kind == refs[j].ref.Kind {
+			if refs[i].ref.ID == refs[j].ref.ID {
+				return rawMapStableKey(refs[i].ref.Extra) < rawMapStableKey(refs[j].ref.Extra)
+			}
 			return refs[i].ref.ID < refs[j].ref.ID
 		}
 		return refs[i].ref.Kind < refs[j].ref.Kind
@@ -282,7 +286,10 @@ func normalizedEdges(in []RelationshipEdge) []RelationshipEdge {
 			},
 			Extra: cloneRawMessages(in[i].Extra),
 		}
-		key := edge.Kind + "\x00" + edge.From.Kind + "\x00" + edge.From.ID + "\x00" + edge.To.Kind + "\x00" + edge.To.ID
+		fromExtraKey := rawMapStableKey(edge.From.Extra)
+		toExtraKey := rawMapStableKey(edge.To.Extra)
+		edgeExtraKey := rawMapStableKey(edge.Extra)
+		key := edge.Kind + "\x00" + edge.From.Kind + "\x00" + edge.From.ID + "\x00" + fromExtraKey + "\x00" + edge.To.Kind + "\x00" + edge.To.ID + "\x00" + toExtraKey + "\x00" + edgeExtraKey
 		if _, ok := seen[key]; ok {
 			continue
 		}
@@ -299,10 +306,19 @@ func normalizedEdges(in []RelationshipEdge) []RelationshipEdge {
 		if edges[i].edge.From.ID != edges[j].edge.From.ID {
 			return edges[i].edge.From.ID < edges[j].edge.From.ID
 		}
+		if left, right := rawMapStableKey(edges[i].edge.From.Extra), rawMapStableKey(edges[j].edge.From.Extra); left != right {
+			return left < right
+		}
 		if edges[i].edge.To.Kind != edges[j].edge.To.Kind {
 			return edges[i].edge.To.Kind < edges[j].edge.To.Kind
 		}
-		return edges[i].edge.To.ID < edges[j].edge.To.ID
+		if edges[i].edge.To.ID != edges[j].edge.To.ID {
+			return edges[i].edge.To.ID < edges[j].edge.To.ID
+		}
+		if left, right := rawMapStableKey(edges[i].edge.To.Extra), rawMapStableKey(edges[j].edge.To.Extra); left != right {
+			return left < right
+		}
+		return rawMapStableKey(edges[i].edge.Extra) < rawMapStableKey(edges[j].edge.Extra)
 	})
 	out := make([]RelationshipEdge, 0, len(edges))
 	for i := range edges {
@@ -453,3 +469,30 @@ func cloneRawMessages(in map[string]json.RawMessage) map[string]json.RawMessage
 	}
 	return out
 }
+
+func rawMapStableKey(in map[string]json.RawMessage) string {
+	if len(in) == 0 {
+		return ""
+	}
+	keys := make([]string, 0, len(in))
+	for k := range in {
+		keys = append(keys, k)
+	}
+	sort.Strings(keys)
+	var b strings.Builder
+	for i := range keys {
+		key := keys[i]
+		val := in[key]
+		canonical := val
+		if len(val) > 0 {
+			if normalized, err := canon.Canonicalize(val, canon.DomainJSON); err == nil {
+				canonical = normalized
+			}
+		}
+		b.WriteString(key)
+		b.WriteByte('\x1f')
+		b.Write(canonical)
+		b.WriteByte('\x1e')
+	}
+	return b.String()
+}
diff --git a/core/record/record_test.go b/core/record/record_test.go
index 9e2fadf..c9ac222 100644
--- a/core/record/record_test.go
+++ b/core/record/record_test.go
@@ -260,6 +260,53 @@ func TestNormalizedEdgesStableSortAndDedup(t *testing.T) {
 	require.Nil(t, normalizedEdges(nil))
 }
 
+func TestNormalizedRefsKeepsDistinctAdditiveMetadata(t *testing.T) {
+	refs := []RelationshipRef{
+		{Kind: "agent", ID: "agent:a", Extra: map[string]json.RawMessage{"tag": json.RawMessage(`"alpha"`)}},
+		{Kind: "agent", ID: "agent:a", Extra: map[string]json.RawMessage{"tag": json.RawMessage(`"beta"`)}},
+		{Kind: "agent", ID: "agent:a", Extra: map[string]json.RawMessage{"tag": json.RawMessage(`"alpha"`)}},
+	}
+	normalized := normalizedRefs(refs)
+	require.Len(t, normalized, 2)
+	require.Equal(t, `"alpha"`, string(normalized[0].Extra["tag"]))
+	require.Equal(t, `"beta"`, string(normalized[1].Extra["tag"]))
+}
+
+func TestNormalizedEdgesKeepsDistinctAdditiveMetadata(t *testing.T) {
+	edges := []RelationshipEdge{
+		{
+			Kind: "calls",
+			From: RelationshipRef{Kind: "agent", ID: "agent:a", Extra: map[string]json.RawMessage{"ctx": json.RawMessage(`"a"`)}},
+			To:   RelationshipRef{Kind: "tool", ID: "tool:x"},
+			Extra: map[string]json.RawMessage{
+				"label": json.RawMessage(`"first"`),
+			},
+		},
+		{
+			Kind: "calls",
+			From: RelationshipRef{Kind: "agent", ID: "agent:a", Extra: map[string]json.RawMessage{"ctx": json.RawMessage(`"b"`)}},
+			To:   RelationshipRef{Kind: "tool", ID: "tool:x"},
+			Extra: map[string]json.RawMessage{
+				"label": json.RawMessage(`"second"`),
+			},
+		},
+		{
+			Kind: "calls",
+			From: RelationshipRef{Kind: "agent", ID: "agent:a", Extra: map[string]json.RawMessage{"ctx": json.RawMessage(`"a"`)}},
+			To:   RelationshipRef{Kind: "tool", ID: "tool:x"},
+			Extra: map[string]json.RawMessage{
+				"label": json.RawMessage(`"first"`),
+			},
+		},
+	}
+	normalized := normalizedEdges(edges)
+	require.Len(t, normalized, 2)
+	require.Equal(t, `"a"`, string(normalized[0].From.Extra["ctx"]))
+	require.Equal(t, `"first"`, string(normalized[0].Extra["label"]))
+	require.Equal(t, `"b"`, string(normalized[1].From.Extra["ctx"]))
+	require.Equal(t, `"second"`, string(normalized[1].Extra["label"]))
+}
+
 func TestComputeHashIncludesRelationshipAndLegacyAlias(t *testing.T) {
 	base := &Record{
 		RecordID:      "prf-test",