Fix #33670

src/vs/platform/configuration/common/configurationRegistry.ts

@@ -62,6 +62,7 @@ export interface IConfigurationPropertySchema extends IJSONSchema {
 	overridable?: boolean;
 	isExecutable?: boolean;
 	scope?: ConfigurationScope;
+	isFromExtensions?: boolean;
 }
 
 export interface IConfigurationNode {

src/vs/workbench/services/configuration/node/configuration.ts

@@ -182,6 +182,7 @@ function validateProperties(configuration: IConfigurationNode, collector: Extens
 			const message = validateProperty(key);
 			const propertyConfiguration = configuration.properties[key];
 			propertyConfiguration.scope = propertyConfiguration.scope && propertyConfiguration.scope.toString() === 'resource' ? ConfigurationScope.RESOURCE : ConfigurationScope.WINDOW;
+			propertyConfiguration.isFromExtensions = true;
 			if (message) {
 				collector.warn(message);
 				delete properties[key];

src/vs/workbench/services/workspace/node/workspaceEditingService.ts

@@ -186,7 +186,7 @@ export class WorkspaceEditingService implements IWorkspaceEditingService {
 		const configurationProperties = Registry.as<IConfigurationRegistry>(ConfigurationExtensions.Configuration).getConfigurationProperties();
 		const targetWorkspaceConfiguration = {};
 		for (const key of this.workspaceConfigurationService.keys().workspace) {
-			if (configurationProperties[key] && configurationProperties[key].scope === ConfigurationScope.WINDOW) {
+			if (configurationProperties[key] && !configurationProperties[key].isFromExtensions && configurationProperties[key].scope === ConfigurationScope.WINDOW) {
 				targetWorkspaceConfiguration[key] = this.workspaceConfigurationService.lookup(key).workspace;
 			}
 		}