Deep Linking only working if app is running

This is correct behavior. You should handle it in appliction(_: didFinishLaunchingWithOptions:)

func application(_ application: UIApplication, didFinishLaunchingWithOptions launchOptions: [UIApplicationLaunchOptionsKey: Any]?) -> Bool {
    // Override point for customization after application launch.
    if let url = launchOptions[.url] as? URL, let annotation = launchOptions[.annotation] {
        return self.application(application, open: url, sourceApplication: launchOptions[.sourceApplication] as? String, annotation: annotation)
    }
    return true
}