diff --git a/gitnexus/src/core/kuzu/kuzu-adapter.ts b/gitnexus/src/core/kuzu/kuzu-adapter.ts
index 78e48bf27..f39d15b0d 100644
--- a/gitnexus/src/core/kuzu/kuzu-adapter.ts
+++ b/gitnexus/src/core/kuzu/kuzu-adapter.ts
@@ -582,15 +582,16 @@ export const loadExistingGraph = async (
       const fromId = str(row.fromId ?? row[0]);
       const toId = str(row.toId ?? row[1]);
       if (!nodeIdSet.has(fromId) || !nodeIdSet.has(toId)) continue;
+      // All relationships are regenerated by the incremental pipeline:
+      // CONTAINS (processStructure), IMPORTS/CALLS/EXTENDS/IMPLEMENTS
+      // (full import/call/heritage), MEMBER_OF/STEP_IN_PROCESS (communities/processes).
+      // Only keep DEFINES for unchanged nodes (File -> code element).
       const type = str(row.type ?? row[2]);
-      // Only keep DEFINES (intra-file, deterministic IDs, only re-created for changed files).
-      // Everything else is regenerated:
-      // - CONTAINS: by processStructure on all files
-      // - IMPORTS, CALLS, EXTENDS, IMPLEMENTS: by full import/call/heritage on all files
-      // - MEMBER_OF, STEP_IN_PROCESS: by community/process detection
       if (type !== 'DEFINES') continue;
+      // For DEFINES: use the canonical ID format to avoid duplicates with freshly parsed results
+      const canonicalId = `DEFINES:${fromId}->${toId}`;
       relationships.push({
-        id: `${fromId}_${type}_${toId}`,
+        id: canonicalId,
         sourceId: fromId,
         targetId: toId,
         type: type as any,