diff --git a/understand-anything-plugin/packages/dashboard/src/utils/__tests__/elk-layout.test.ts b/understand-anything-plugin/packages/dashboard/src/utils/__tests__/elk-layout.test.ts
index fc13b5977..ffe0d4f81 100644
--- a/understand-anything-plugin/packages/dashboard/src/utils/__tests__/elk-layout.test.ts
+++ b/understand-anything-plugin/packages/dashboard/src/utils/__tests__/elk-layout.test.ts
@@ -42,6 +42,107 @@ describe("repairElkInput", () => {
     expect(issues.some((i) => i.level === "dropped" && /edge/.test(i.message))).toBe(true);
   });
 
+  it("drops edges pointing at children removed by the orphan-child pass", () => {
+    const input: ElkInput = {
+      id: "root",
+      children: [
+        { id: "a", width: 1, height: 1 },
+        { id: "orphan", width: 1, height: 1, parentId: "ghost" } as ElkInput["children"][0] & { parentId: string },
+      ],
+      edges: [{ id: "e1", sources: ["a"], targets: ["orphan"] }],
+    };
+    const { input: out, issues } = repairElkInput(input);
+    expect(out.children!.find((c) => c.id === "orphan")).toBeUndefined();
+    expect(out.edges).toHaveLength(0);
+    expect(issues.some((i) => i.level === "dropped" && i.category === "elk-orphan-edge")).toBe(true);
+  });
+
+  it("drops edges pointing at a node removed by the containment-cycle pass", () => {
+    // x and y mutually contain each other (via shared ids at different levels),
+    // so fillParents records parentOf(x)=y and parentOf(y)=x and the cycle pass
+    // removes both. An edge targeting x must then be reconciled away by step 5.
+    const input: ElkInput = {
+      id: "root",
+      children: [
+        { id: "x", width: 1, height: 1, children: [{ id: "y", width: 1, height: 1 }] },
+        { id: "y", width: 1, height: 1, children: [{ id: "x", width: 1, height: 1 }] },
+        { id: "a", width: 1, height: 1 },
+      ] as ElkInput["children"],
+      edges: [{ id: "e1", sources: ["a"], targets: ["x"] }],
+    };
+    const { input: out, issues } = repairElkInput(input);
+    expect(out.children!.find((c) => c.id === "x")).toBeUndefined();
+    expect(out.children!.find((c) => c.id === "y")).toBeUndefined();
+    expect(out.edges).toHaveLength(0);
+    expect(
+      issues.some((i) => i.level === "dropped" && i.category === "elk-containment-cycle"),
+    ).toBe(true);
+    expect(
+      issues.some(
+        (i) =>
+          i.level === "dropped" &&
+          i.category === "elk-orphan-edge" &&
+          /\be1\b/.test(i.message),
+      ),
+    ).toBe(true);
+  });
+
+  it("drops edges pointing at a nested grandchild carried out by an orphan-child parent drop", () => {
+    // Parent `p` has a missing parentId, so the orphan-child pass (step 3) drops
+    // it AND its whole subtree, including the nested grandchild `gc`. An edge
+    // targeting `gc` must be reconciled away by step 5 even though no pass
+    // explicitly tracked `gc` being removed.
+    const input: ElkInput = {
+      id: "root",
+      children: [
+        { id: "a", width: 1, height: 1 },
+        {
+          id: "p",
+          width: 1,
+          height: 1,
+          parentId: "ghost",
+          children: [{ id: "gc", width: 1, height: 1 }],
+        } as ElkInput["children"][0] & { parentId: string },
+      ],
+      edges: [{ id: "e1", sources: ["a"], targets: ["gc"] }],
+    };
+    const { input: out, issues } = repairElkInput(input);
+    expect(out.children!.find((c) => c.id === "p")).toBeUndefined();
+    expect(out.edges).toHaveLength(0);
+    expect(
+      issues.some(
+        (i) =>
+          i.level === "dropped" &&
+          i.category === "elk-orphan-edge" &&
+          /\be1\b/.test(i.message),
+      ),
+    ).toBe(true);
+  });
+
+  it("includes dropped edge ids in the orphan-edge message so distinct losses survive level|message dedupe", () => {
+    const runOne: ElkInput = {
+      id: "root",
+      children: [{ id: "a", width: 1, height: 1 }],
+      edges: [{ id: "e1", sources: ["a"], targets: ["ghost"] }],
+    };
+    const runTwo: ElkInput = {
+      id: "root",
+      children: [{ id: "a", width: 1, height: 1 }],
+      edges: [{ id: "e2", sources: ["a"], targets: ["ghost"] }],
+    };
+    const msgOne = repairElkInput(runOne).issues.find(
+      (i) => i.category === "elk-orphan-edge",
+    )!.message;
+    const msgTwo = repairElkInput(runTwo).issues.find(
+      (i) => i.category === "elk-orphan-edge",
+    )!.message;
+    expect(msgOne).toContain("e1");
+    expect(msgTwo).toContain("e2");
+    // Distinct dropped edges must yield distinct messages, otherwise store.ts
+    // appendLayoutIssues (dedupe by `level|message`) swallows the second loss.
+    expect(msgOne).not.toEqual(msgTwo);
+  });
+
   it("drops children referencing nonexistent parents", () => {
     const input: ElkInput = {
       id: "root",
diff --git a/understand-anything-plugin/packages/dashboard/src/utils/elk-layout.ts b/understand-anything-plugin/packages/dashboard/src/utils/elk-layout.ts
index 8bc9f8628..5e7eff7e8 100644
--- a/understand-anything-plugin/packages/dashboard/src/utils/elk-layout.ts
+++ b/understand-anything-plugin/packages/dashboard/src/utils/elk-layout.ts
@@ -140,28 +140,7 @@ export function repairElkInput(
     maybeThrow(strict, issue);
   }
 
-  // 4. dropOrphanEdges
-  let orphanEdges = 0;
-  const edges = input.edges.filter((e) => {
-    const ok = e.sources.every((s) => allIds.has(s)) &&
-      e.targets.every((t) => allIds.has(t));
-    if (!ok) {
-      orphanEdges++;
-      return false;
-    }
-    return true;
-  });
-  if (orphanEdges > 0) {
-    const issue = makeIssue(
-      "dropped",
-      "elk-orphan-edge",
-      `Dropped ${orphanEdges} edge(s) referencing nonexistent nodes.`,
-    );
-    issues.push(issue);
-    maybeThrow(strict, issue);
-  }
-
-  // 5. dropCircularContainment
+  // 4. dropCircularContainment
   const parentOf = new Map<string, string>();
   const fillParents = (children: ElkChild[], parent?: string) => {
     for (const c of children) {
@@ -205,6 +184,53 @@ export function repairElkInput(
     maybeThrow(strict, issue);
   }
 
+  // 5. dropOrphanEdges — this is the single reconciliation point that validates
+  // edges against the FINAL child tree (childrenD). It therefore drops edges
+  // pointing at nodes removed by ANY prior pass: original ghost endpoints, the
+  // orphan-child pass (step 3, which carries dropped parents' whole c.children
+  // subtrees out), and the containment-cycle pass (step 4). Per-pass drop
+  // attribution (which pass removed the endpoint) is deliberately NOT tracked
+  // here; if that traceability is ever needed, the orphan-child/cycle passes
+  // would each return { children, removedIds } and filter their own edges.
+  const finalIds = new Set<string>();
+  const walkFinal = (children: ElkChild[]) => {
+    for (const c of children) {
+      finalIds.add(c.id);
+      if (c.children) walkFinal(c.children);
+    }
+  };
+  walkFinal(childrenD);
+  let orphanEdges = 0;
+  const droppedEdgeIds: string[] = [];
+  const edges = input.edges.filter((e) => {
+    const ok = e.sources.every((s) => finalIds.has(s)) &&
+      e.targets.every((t) => finalIds.has(t));
+    if (!ok) {
+      orphanEdges++;
+      droppedEdgeIds.push(e.id);
+      return false;
+    }
+    return true;
+  });
+  if (orphanEdges > 0) {
+    // Include the dropped edge ids so distinct losses across re-layouts produce
+    // distinct messages — store.ts appendLayoutIssues dedupes by `level|message`,
+    // so a generic count would swallow a fresh single-edge drop on a later run.
+    const MAX_LISTED = 20;
+    const listed = droppedEdgeIds.slice(0, MAX_LISTED).join(", ");
+    const suffix =
+      droppedEdgeIds.length > MAX_LISTED
+        ? `${listed}, …(+${droppedEdgeIds.length - MAX_LISTED} more)`
+        : listed;
+    const issue = makeIssue(
+      "dropped",
+      "elk-orphan-edge",
+      `Dropped ${orphanEdges} edge(s) referencing nonexistent nodes: ${suffix}.`,
+    );
+    issues.push(issue);
+    maybeThrow(strict, issue);
+  }
+
   return {
     input: { ...input, children: childrenD, edges },
     issues,