Please correct me if I wrongly understood your issue .
You created a report in Desktop and applied the persistent filters . Then you published the report to Service , and created an app . Persistent filters worked well in app . Then you created a report in Service with the shared dataset in the same workspace , and updated the app , but persistent filters didn't work , right ?
I tested it as I understood it , enabled persistent filters , published the report to the app , and tested it in the app , when I filtered the data, then switched to other reports , and then switched back to the filtered one report, all filters are gone .