In our case we deleted the apps in both slots and re-deployed.
Before that we tried an number of cleanup operations in Azure using the Kudo debug console without any progress. The warning message turned up when we activated the staging slot in our TEST environment, we don't use the staging slot in our DEV and there we didn't get the message. We have had this warning message for 4 days, so to us it looks like it hadn't gone away on its own.