My app has 2 activities. The root activity of the app is the MainActivity. If credentials are missing or invalid the user will be redirected to the LoginActivity while finishing
allowTaskReparenting = true
https://developer.android.com/guide/topics/manifest/activity-element#reparent
May have solved your issue (with this set, when you return to the forwarding app, you will be returning to the activity natural for that app and not the activity that it launched in the target app) Not too sure why true isn't the default for this...
Well thanks to the tip by orelzion I managed to solve this issue:
I did create a new DeepLinkActivity which started the MainActivity (which i changhed the launch mode from "singleTask" to "singleTop") with the following flags:
Intent.FLAG_ACTIVITY_REORDER_TO_FRONT | Intent.FLAG_ACTIVITY_CLEAR_TASK | Intent.FLAG_ACTIVITY_NEW_TASK
All flags are needed in order to take care of a few issues that came up while trying to fix my problem.