Symptoms

When update the app and run registration wizard for site in SPS site collection, the following error was thrown:
SmartObject Server Exception: Error refreshing Service Instance ‘Site’. Service returned : 'Access denied. You do not have permission to perform this action or access this resource.Failed to initialize the Context: URL: Site URL Username: Correlation ID: f3c36b9d-8022-2000-36bc-5a79488228cc Error Details: Method: SharePointService.initializeContext '.

 

Diagnoses

After the user grants consent during the Registration wizard, an OAuth token gets saved in the database. The saved token will be used for all future calls from Appit to AAD and SharePoint Online until it expires.
This error was caused by previous global admin account that originally ran registration wizard was removed from Site Collection admin.

 

Resolution

Adding this account to Site collection admin allow the registration wizard to be run successfully.