fix(core): Persist scalar custom fields in updateGlobalSettings with relations

Save the entity to DB before calling updateRelations so that when
updateRelations re-fetches the entity, it picks up the already-persisted
scalar custom field values instead of stale DB values.

Fixes #4342

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: biggamesmallworld

packages/core/e2e/custom-field-relations.e2e-spec.ts

@@ -710,6 +710,37 @@ describe('Custom field relations', () => {
                 `);
                 assertCustomFieldIds(updateGlobalSettings.customFields, 'T_2', ['T_3', 'T_4']);
             });
+
+            // https://github.com/vendurehq/vendure/issues/4342
+            it('scalar custom fields persist when updating alongside relations', async () => {
+                const { updateGlobalSettings } = await adminClient.query(gql`
+                    mutation {
+                        updateGlobalSettings(
+                            input: {
+                                customFields: { primitive: "updated", singleId: "T_3", multiIds: ["T_1", "T_2"] }
+                            }
+                        ) {
+                            ... on GlobalSettings {
+                                id
+                                ${customFieldsSelection}
+                            }
+                        }
+                    }
+                `);
+                expect(updateGlobalSettings.customFields.primitive).toBe('updated');
+                assertCustomFieldIds(updateGlobalSettings.customFields, 'T_3', ['T_1', 'T_2']);
+
+                // Verify the scalar value actually persisted by re-querying
+                const { globalSettings } = await adminClient.query(gql`
+                    query {
+                        globalSettings {
+                            ${customFieldsSelection}
+                        }
+                    }
+                `);
+                expect(globalSettings.customFields.primitive).toBe('updated');
+                assertCustomFieldIds(globalSettings.customFields, 'T_3', ['T_1', 'T_2']);
+            });
         });
 
         describe('Order entity', () => {

packages/core/src/service/services/global-settings.service.ts

@@ -78,7 +78,8 @@ export class GlobalSettingsService {
         const settings = await this.getSettings(ctx);
         await this.eventBus.publish(new GlobalSettingsEvent(ctx, settings, input));
         patchEntity(settings, input);
-        await this.customFieldRelationService.updateRelations(ctx, GlobalSettings, input, settings);
-        return this.connection.getRepository(ctx, GlobalSettings).save(settings);
+        const savedSettings = await this.connection.getRepository(ctx, GlobalSettings).save(settings);
+        await this.customFieldRelationService.updateRelations(ctx, GlobalSettings, input, savedSettings);
+        return savedSettings;
     }
 }