diff --git a/web/app/components/evaluation/__tests__/store.spec.ts b/web/app/components/evaluation/__tests__/store.spec.ts
index 0557f52945..ee7938d661 100644
--- a/web/app/components/evaluation/__tests__/store.spec.ts
+++ b/web/app/components/evaluation/__tests__/store.spec.ts
@@ -258,6 +258,7 @@ describe('evaluation store', () => {
     ])
     expect(hydratedState.metrics[1].kind).toBe('custom-workflow')
     expect(hydratedState.metrics[1].customConfig?.workflowId).toBe('workflow-precision-review')
+    expect(hydratedState.metrics[1].customConfig?.workflowAppId).toBe('workflow-precision-review')
     expect(hydratedState.metrics[1].customConfig?.mappings[0].inputVariableId).toBe('query')
     expect(hydratedState.metrics[1].customConfig?.mappings[0].outputVariableId).toBe('answer')
     expect(hydratedState.metrics[1].customConfig?.outputs).toEqual([{ id: 'reason', valueType: 'string' }])
diff --git a/web/app/components/evaluation/components/custom-metric-editor/__tests__/index.spec.tsx b/web/app/components/evaluation/components/custom-metric-editor/__tests__/index.spec.tsx
index 5f2c026908..e72048dc6d 100644
--- a/web/app/components/evaluation/components/custom-metric-editor/__tests__/index.spec.tsx
+++ b/web/app/components/evaluation/components/custom-metric-editor/__tests__/index.spec.tsx
@@ -199,6 +199,10 @@ describe('CustomMetricEditorCard', () => {
     mockUseSnippetPublishedWorkflow.mockReturnValue({ data: undefined })
   })
 
+  afterEach(() => {
+    vi.restoreAllMocks()
+  })
+
   // Verify the selected evaluation workflow still drives the output summary section.
   describe('Outputs', () => {
     it('should render the selected workflow outputs from the end node', () => {
@@ -274,6 +278,33 @@ describe('CustomMetricEditorCard', () => {
 
   // Verify mapping rows use workflow start variables on the left and current published graph variables on the right.
   describe('Variable Mapping', () => {
+    it('should preserve saved mappings and outputs while the selected workflow is loading', () => {
+      const baseMetric = createMetric()
+      const metric = {
+        ...baseMetric,
+        customConfig: {
+          ...baseMetric.customConfig!,
+          outputs: [{ id: 'score', valueType: 'number' }],
+        },
+      }
+      const syncMappingsSpy = vi.spyOn(useEvaluationStore.getState(), 'syncCustomMetricMappings')
+      const syncOutputsSpy = vi.spyOn(useEvaluationStore.getState(), 'syncCustomMetricOutputs')
+
+      mockUseAppWorkflow.mockReturnValue({ data: undefined })
+
+      render(
+        <CustomMetricEditorCard
+          resourceType="apps"
+          resourceId="app-under-test"
+          metric={metric}
+        />,
+      )
+
+      expect(screen.getByText('Evaluation Workflow')).toBeInTheDocument()
+      expect(syncMappingsSpy).not.toHaveBeenCalled()
+      expect(syncOutputsSpy).not.toHaveBeenCalled()
+    })
+
     it('should pass the current app published graph and saved selector values to the picker', () => {
       const selectedWorkflow = createWorkflow([
         createStartNode(),
diff --git a/web/app/components/evaluation/components/custom-metric-editor/index.tsx b/web/app/components/evaluation/components/custom-metric-editor/index.tsx
index 694e48d310..b76d866a50 100644
--- a/web/app/components/evaluation/components/custom-metric-editor/index.tsx
+++ b/web/app/components/evaluation/components/custom-metric-editor/index.tsx
@@ -44,6 +44,7 @@ const getWorkflowOutputs = (nodes?: Array<Node>) => {
         .map(output => ({
           id: output.variable,
           valueType: typeof output.value_type === 'string' ? output.value_type : null,
+          nodeId: endNode.id,
           nodeTitle: typeof endNode.data.title === 'string' && endNode.data.title ? endNode.data.title : 'End',
         }))
     })
@@ -110,9 +111,10 @@ const CustomMetricEditorCard = ({
   ])
   const inputVariableIds = useMemo(() => inputVariables.map(variable => variable.id), [inputVariables])
   const isConfigured = isCustomMetricConfigured(metric)
+  const isSelectedWorkflowLoaded = !!selectedWorkflow
 
   useEffect(() => {
-    if (!metric.customConfig?.workflowId)
+    if (!metric.customConfig?.workflowId || !isSelectedWorkflowLoaded)
       return
 
     const currentInputVariableIds = metric.customConfig.mappings
@@ -125,10 +127,10 @@ const CustomMetricEditorCard = ({
     }
 
     syncCustomMetricMappings(resourceType, resourceId, metric.id, inputVariableIds)
-  }, [inputVariableIds, metric.customConfig?.mappings, metric.customConfig?.workflowId, metric.id, resourceId, resourceType, syncCustomMetricMappings])
+  }, [inputVariableIds, isSelectedWorkflowLoaded, metric.customConfig?.mappings, metric.customConfig?.workflowId, metric.id, resourceId, resourceType, syncCustomMetricMappings])
 
   useEffect(() => {
-    if (!metric.customConfig?.workflowId)
+    if (!metric.customConfig?.workflowId || !isSelectedWorkflowLoaded)
       return
 
     const currentOutputs = metric.customConfig.outputs
@@ -142,7 +144,7 @@ const CustomMetricEditorCard = ({
     }
 
     syncCustomMetricOutputs(resourceType, resourceId, metric.id, workflowOutputs)
-  }, [metric.customConfig?.outputs, metric.customConfig?.workflowId, metric.id, resourceId, resourceType, syncCustomMetricOutputs, workflowOutputs])
+  }, [isSelectedWorkflowLoaded, metric.customConfig?.outputs, metric.customConfig?.workflowId, metric.id, resourceId, resourceType, syncCustomMetricOutputs, workflowOutputs])
 
   if (!metric.customConfig)
     return null
@@ -197,7 +199,7 @@ const CustomMetricEditorCard = ({
           </div>
           <div className="flex flex-wrap items-center gap-y-1 px-2 py-2 system-xs-regular text-text-tertiary">
             {workflowOutputs.map((output, index) => (
-              <div key={`${output.nodeTitle}-${output.id}-${index}`} className="flex items-center">
+              <div key={`${output.nodeId}-${output.id}`} className="flex items-center">
                 <span className="px-1 system-xs-medium text-text-secondary">{output.id}</span>
                 {output.valueType && (
                   <span>{output.valueType}</span>
diff --git a/web/app/components/evaluation/store-utils.ts b/web/app/components/evaluation/store-utils.ts
index ce2ecf7f18..5e670ece24 100644
--- a/web/app/components/evaluation/store-utils.ts
+++ b/web/app/components/evaluation/store-utils.ts
@@ -130,7 +130,7 @@ const normalizeCustomMetricMappings = (
 const normalizeCustomMetricOutputs = (
   value: EvaluationCustomizedMetric['output_fields'],
 ) => {
-  if (!value)
+  if (!Array.isArray(value))
     return []
 
   return value
@@ -165,6 +165,7 @@ const normalizeCustomMetric = (
       ? {
           ...customMetric.customConfig,
           workflowId,
+          workflowAppId: workflowId,
           mappings: normalizeCustomMetricMappings(value.input_fields),
           outputs: normalizeCustomMetricOutputs(value.output_fields),
         }