So, we had the same problem when we updated the XSUAA Connector in our app.
The problem: User X could no longer sign into the app after the module update.
The solution: Remove the Account of User X
Why: The new module wants to create a SapUser object when User X signs in for the first time after the update. But it can't, because there is already an Account with the same Name. Both Account and SapUser are specializations of System.User and there can be no two objects with the same Name.
Why we went back to the old XSUAA Connector for the moment: Removing all Accounts caused some microflows to stop working, because in them are retrieves based on Account. We have to migrate those microflows (and some pages) from Account to SapUser before we can deploy the app with the new XSUAA Connector.