Disabling and re-enabling a core extension removes it from the navigation menu and from SK
If you disabled and re-enable a core extension, you lose the relevant navigation menu item and you lose some of the relevant entities in SK. For example, if you disable and re-enable civi_mail, you lose the Mailing menu item and the Mailings and Outbound Mailings entities disappear from SearchKit (but Mailing Bounces, etc are still present). Similar with civi_member. Cache clearing or menu rebuilding doesn't help. On dmaster.