Your site will be inaccessible during maintenance and usually, it is recommended to stop/restart IIS out of working hours when almost no one uses your site. Existing data should not be lost, but site visitors will lose connection during some action (form submission etc.) and Sitecore analytics will not be triggered.
UsuallyIf you need to stop your sites, then, usually, it is recommended to stop XP instances first (CD instances first, then CM), then you can stop xConnect instances, and then after maintenance, you can start xConnect instances first and then XP instances (CM first, then CD instances).