diff --git a/x-pack/plugins/lens/public/indexpattern_datasource/operations/layer_helpers.test.ts b/x-pack/plugins/lens/public/indexpattern_datasource/operations/layer_helpers.test.ts
index 62cce21ead636..34e2eb2c90122 100644
--- a/x-pack/plugins/lens/public/indexpattern_datasource/operations/layer_helpers.test.ts
+++ b/x-pack/plugins/lens/public/indexpattern_datasource/operations/layer_helpers.test.ts
@@ -2089,6 +2089,38 @@ describe('state_helpers', () => {
       });
     });
 
+    it('should remove operations indirectly referencing unavailable fields', () => {
+      const layer: IndexPatternLayer = {
+        columnOrder: ['col1', 'col2'],
+        columns: {
+          col1: {
+            label: '',
+            dataType: 'number',
+            operationType: 'moving_average',
+            isBucketed: false,
+            scale: 'ratio',
+            references: ['col2'],
+            timeScale: undefined,
+            filter: undefined,
+            params: {
+              window: 7,
+            },
+          },
+          col2: {
+            dataType: 'number',
+            isBucketed: false,
+            label: '',
+            operationType: 'average',
+            sourceField: 'xxx',
+          },
+        },
+        indexPatternId: 'original',
+      };
+      const updatedLayer = updateLayerIndexPattern(layer, newIndexPattern);
+      expect(updatedLayer.columnOrder).toEqual([]);
+      expect(updatedLayer.columns).toEqual({});
+    });
+
     it('should remove operations referencing fields with insufficient capabilities', () => {
       const layer: IndexPatternLayer = {
         columnOrder: ['col1', 'col2'],
diff --git a/x-pack/plugins/lens/public/indexpattern_datasource/operations/layer_helpers.ts b/x-pack/plugins/lens/public/indexpattern_datasource/operations/layer_helpers.ts
index 7853b7da7956e..1661e5de8248e 100644
--- a/x-pack/plugins/lens/public/indexpattern_datasource/operations/layer_helpers.ts
+++ b/x-pack/plugins/lens/public/indexpattern_datasource/operations/layer_helpers.ts
@@ -929,9 +929,17 @@ export function updateLayerIndexPattern(
   layer: IndexPatternLayer,
   newIndexPattern: IndexPattern
 ): IndexPatternLayer {
-  const keptColumns: IndexPatternLayer['columns'] = _.pickBy(layer.columns, (column) =>
-    isColumnTransferable(column, newIndexPattern)
-  );
+  const keptColumns: IndexPatternLayer['columns'] = _.pickBy(layer.columns, (column) => {
+    if ('references' in column) {
+      return (
+        isColumnTransferable(column, newIndexPattern) &&
+        column.references.every((columnId) =>
+          isColumnTransferable(layer.columns[columnId], newIndexPattern)
+        )
+      );
+    }
+    return isColumnTransferable(column, newIndexPattern);
+  });
   const newColumns: IndexPatternLayer['columns'] = _.mapValues(keptColumns, (column) => {
     const operationDefinition = operationDefinitionMap[column.operationType];
     return operationDefinition.transfer