In order to delete several waypoints, in other words a section of the tour, you can use the selection tool on the upper left corner of the map (a dotted rectangle with a cursor in it). With this tool you can select various waypoints in order to remove them with the delete key or move them with your cursor. This is convenient especially when editing GPX tracks, which consist of very many waypoints.
In order to delete one individual waypoint, you can either choose the “X” next to the point or right click on the point and choose “delete point”. Here you can also “delete the entire geometry“.
Did you accidentally delete a waypoint? No problem! Using right-click on the point in the map you can “restore” or “undo” an action.