Fixed it! There's a delegate method called by the splitview when its popover is going to present a view controller, here it is:
//-------------------------------------------------------------------------------------
// splitViewController:popoverController:willPresentViewController:
//-------------------------------------------------------------------------------------
- (void)splitViewController:(UISplitViewController *)svc
popoverController:(UIPopoverController *)pc
willPresentViewController:(UIViewController *)aViewController
{
[self.popoverSettings dismissPopoverAnimated:YES]; //dismiss the other popover here
}
Apple's documentation here