diff --git a/packages/api/src/agents/discovery.spec.ts b/packages/api/src/agents/discovery.spec.ts
index 337f9bd059..5cc811d551 100644
--- a/packages/api/src/agents/discovery.spec.ts
+++ b/packages/api/src/agents/discovery.spec.ts
@@ -202,6 +202,40 @@ describe('discoverConnectedAgents', () => {
     expect(result.edges.map((e) => e.to)).toEqual(['B']);
   });
 
+  it('drops edges whose `from` references a skipped agent (bidirectional graph)', async () => {
+    // Orchestrator A with bidirectional handoffs A<->B. B is inaccessible,
+    // so `A -> B` and `B -> A` must both be filtered — otherwise `B -> A`
+    // leaks into createRun and triggers `Found edge ending at unknown node`.
+    const edges: GraphEdge[] = [
+      { from: 'A', to: 'B', edgeType: 'handoff' },
+      { from: 'B', to: 'A', edgeType: 'handoff' },
+    ];
+    const primaryConfig = makeConfig('A', edges);
+
+    const getAgent = jest.fn(async () => makeAgent('B', []));
+    const checkPermission = jest.fn().mockResolvedValue(false);
+
+    const result = await discoverConnectedAgents(
+      {
+        req: makeReq(),
+        res: makeRes(),
+        primaryConfig,
+        allowedProviders: new Set(),
+        modelsConfig: { openai: ['gpt-4o'] },
+        loadTools: jest.fn(),
+      },
+      {
+        getAgent,
+        checkPermission,
+        logViolation: jest.fn(),
+        db: {} as never,
+      },
+    );
+
+    expect(result.skippedAgentIds.has('B')).toBe(true);
+    expect(result.edges).toHaveLength(0);
+  });
+
   it('does not re-initialize agents that are already known (dedup)', async () => {
     const edges: GraphEdge[] = [
       { from: 'A', to: 'B', edgeType: 'handoff' },
diff --git a/packages/api/src/agents/edges.spec.ts b/packages/api/src/agents/edges.spec.ts
index b23f00f63f..8912c729b9 100644
--- a/packages/api/src/agents/edges.spec.ts
+++ b/packages/api/src/agents/edges.spec.ts
@@ -131,25 +131,35 @@ describe('edges utilities', () => {
       expect(filterOrphanedEdges(edges, skipped)).toEqual(edges);
     });
 
-    it('should filter out edges with orphaned to targets', () => {
+    it('should filter out edges with orphaned to targets and orphaned from sources', () => {
       const skipped = new Set(['agent_b']);
       const result = filterOrphanedEdges(edges, skipped);
-      // Only filters edges where `to` is in skipped set
       // agent_a -> agent_b (filtered - to=agent_b is skipped)
-      // agent_a -> agent_c (kept - to=agent_c not skipped)
-      // agent_b -> agent_d (kept - to=agent_d not skipped, from is not checked)
-      expect(result).toHaveLength(2);
-      expect(result.map((e) => e.to)).toEqual(['agent_c', 'agent_d']);
+      // agent_a -> agent_c (kept - neither endpoint skipped)
+      // agent_b -> agent_d (filtered - from=agent_b is skipped; a source-side
+      // orphan would otherwise leave the graph referencing an absent agent)
+      expect(result).toHaveLength(1);
+      expect(result[0].to).toBe('agent_c');
     });
 
     it('should filter out multiple orphaned edges', () => {
       const skipped = new Set(['agent_b', 'agent_c']);
       const result = filterOrphanedEdges(edges, skipped);
-      // agent_a -> agent_b (filtered)
-      // agent_a -> agent_c (filtered)
-      // agent_b -> agent_d (kept - to=agent_d not skipped)
+      // agent_a -> agent_b (filtered, to)
+      // agent_a -> agent_c (filtered, to)
+      // agent_b -> agent_d (filtered, from)
+      expect(result).toHaveLength(0);
+    });
+
+    it('should filter edges whose `from` is an array containing a skipped id', () => {
+      const edgesWithArrayFrom: GraphEdge[] = [
+        { from: ['agent_a', 'agent_b'], to: 'agent_d', edgeType: 'handoff' },
+        { from: 'agent_a', to: 'agent_d', edgeType: 'handoff' },
+      ];
+      const skipped = new Set(['agent_b']);
+      const result = filterOrphanedEdges(edgesWithArrayFrom, skipped);
       expect(result).toHaveLength(1);
-      expect(result[0].to).toBe('agent_d');
+      expect(result[0].from).toBe('agent_a');
     });
 
     it('should handle array to values', () => {
diff --git a/packages/api/src/agents/edges.ts b/packages/api/src/agents/edges.ts
index 9a36105b74..2e6d4324e5 100644
--- a/packages/api/src/agents/edges.ts
+++ b/packages/api/src/agents/edges.ts
@@ -30,17 +30,21 @@ export function getEdgeParticipants(edge: GraphEdge): string[] {
 }
 
 /**
- * Filters out edges that reference non-existent (orphaned) agents.
- * Only filters based on the 'to' field since those are the handoff targets.
+ * Filters out edges that reference non-existent (orphaned) agents on
+ * either endpoint. Any edge whose `from` OR `to` references a skipped
+ * agent id is dropped — leaving a source-side orphan in place would
+ * still fail graph compilation with `Found edge ending at unknown node`
+ * because `agents` no longer contains the source.
  */
 export function filterOrphanedEdges(edges: GraphEdge[], skippedAgentIds: Set<string>): GraphEdge[] {
   if (!edges || skippedAgentIds.size === 0) {
     return edges;
   }
-  return edges.filter((edge) => {
-    const toIds = Array.isArray(edge.to) ? edge.to : [edge.to];
-    return !toIds.some((id) => typeof id === 'string' && skippedAgentIds.has(id));
-  });
+  const referencesSkipped = (value: string | string[]): boolean => {
+    const ids = Array.isArray(value) ? value : [value];
+    return ids.some((id) => typeof id === 'string' && skippedAgentIds.has(id));
+  };
+  return edges.filter((edge) => !referencesSkipped(edge.from) && !referencesSkipped(edge.to));
 }
 
 /** Collects all unique agent IDs referenced across an array of edges. */