I cannot remember how I solved this issue. But you can try create a virtual proxy with windows authentication, link main proxy to newly created virtual proxy. And from data connections section in QMC, change connection strings for rest connections or qrs connections like this http://localhost/qrs/... to http://localhost/<newly created virtual proxy's prefix>/qrs/...
If this won't solve your problem, you can import new apps from C:\ProgramData\Qlik\Sense\Repository\DefaultApps. This will create new data connections. You can try the solution I mentioned above on this data connections.
