Should a Business Rule no longer show in the right side pane of your template after the "Business Rules" button has been clicked on, but the place holder still exists. It is most likely due to a user having clicked on the "Undo" button or having pressing Ctrl+Z on the keyboard after having deleted the Business Rule from the template.
Using this undo feature will bring back the Business Rule's place holder into the template but not the Business Rules custom XML. Therefore when the Business Rule tab is opened, it will no longer be listed there but will seem like it should be due to the place holder being present.
It is highly recommended NOT to use the Undo/Ctrl+Z action while working with place holders or smart functionality in templates, rather use the delete buttons the QDG ribbon provides to remove functionality.
Should you know for a fact it is happening without using the Undo/Ctrl+Z, please do not hesitate to contact Support via the helpdesk or, email; email@example.com.