Использование MKAnnotationView.setSelected(_:animated:)
func mapView(_ mapView: MKMapView, didSelect view: MKAnnotationView) {
...
view.setSelected(false, animated: false)
}
Или MKMapView.deselectAnnotation(_:animated:)
func mapView(_ mapView: MKMapView, didSelect view: MKAnnotationView) {
if let selected = view.annotation as? CustomAnnotation {
...
mapView.deselectAnnotation(selected, animated: false)
}
}
Update-1
if let annotationView = mapView.view(for: selected) {
annotationView.setSelected(false, animated: false)
}