ISSUE: When cloning a site, the menu links are updated on the clone when the original is updated.
SYMPTOMS: You've cloned a site to reuse the format and then updated a link in a menu. This updates the link in the other site as well.
RESOLUTION: The menus are copied in the site clone process to point to the exact same base links references. You will need to edit the menus and select the resource they are pointing to using the menu build tool instead. This process will create a new independent link reference. You can avoid this by not using the link option in the original site menus and using the Site, App, or Page functions instead.