All notifications disappearing after opening one of them

By setting the applicationIconBadgeNumber to 0, you also remove every notification from the notification center.

This has also been discussed here: iOS application: how to clear notifications?

Furthermore, it is not possible to programmatically remove a single notification, but from iOS8 on, the OS will handle this for you when a user taps a single notification. This has also been discussed here: Remove single remote notification from Notification Center

If you use OneSignal SDK in your app, and you have the problem of disappearing notifications after opening one, you must add key OneSignal_disable_badge_clearing to the Info.plist file in Xcode, as a Boolean type set to YES.

More info here https://documentation.onesignal.com/docs/badges