diff --git a/Composer/packages/server/src/models/bot/botProject.ts b/Composer/packages/server/src/models/bot/botProject.ts
index d1d0c62532..464730b321 100644
--- a/Composer/packages/server/src/models/bot/botProject.ts
+++ b/Composer/packages/server/src/models/bot/botProject.ts
@@ -242,9 +242,9 @@ export class BotProject implements IBotProject {
       // if endpointKey has not been set, migrate old key to new key
       if (!settings.qna.endpointKey) {
         settings.qna.endpointKey = settings.qna.endpointkey;
+        delete settings.qna.endpointkey;
+        await this.updateEnvSettings(settings);
       }
-      delete settings.qna.endpointkey;
-      await this.updateEnvSettings(settings);
     }
 
     // set these after migrating qna settings to not write them to storage
diff --git a/Composer/packages/server/src/models/settings/defaultSettingManager.ts b/Composer/packages/server/src/models/settings/defaultSettingManager.ts
index b0c77cadab..bc3adc6edc 100644
--- a/Composer/packages/server/src/models/settings/defaultSettingManager.ts
+++ b/Composer/packages/server/src/models/settings/defaultSettingManager.ts
@@ -121,6 +121,7 @@ export class DefaultSettingManager extends FileSettingManager {
         maxImbalanceRatio: -1,
       },
       skill: {},
+      skillConfiguration: {},
       defaultLanguage: 'en-us',
       languages: ['en-us'],
       customFunctions: [],
diff --git a/extensions/packageManager/src/node/index.ts b/extensions/packageManager/src/node/index.ts
index 6bccb18806..90af31cc1c 100644
--- a/extensions/packageManager/src/node/index.ts
+++ b/extensions/packageManager/src/node/index.ts
@@ -386,7 +386,7 @@ export default async (composer: IExtensionRegistration): Promise<void> => {
                 newlyInstalledPlugin &&
                 !currentProject.settings.runtimeSettings?.components?.find((p) => p.name === newlyInstalledPlugin.name)
               ) {
-                const newSettings = currentProject.settings;
+                const newSettings = await currentProject.getEnvSettings();
                 if (!newSettings.runtimeSettings) {
                   newSettings.runtimeSettings = {
                     components: [],
@@ -475,7 +475,7 @@ export default async (composer: IExtensionRegistration): Promise<void> => {
 
           // update the settings.components array
           if (currentProject.settings.runtimeSettings?.components?.find((p) => p.name === packageName)) {
-            const newSettings = currentProject.settings;
+            const newSettings = await currentProject.getEnvSettings();
             newSettings.runtimeSettings.components = newSettings.runtimeSettings.components.filter(
               (p) => p.name !== packageName
             );