Without seeing it I assume the controls are still children of the group but are positioned outside its bounds. Most times the only way to get them back in place is by the modulator list, where you can then edit the bounds by hand. Also, when you copy a group then only the group modulator is copied, not the contained modulators. When you paste a modulator that you´ve copied from a group, it is pasted as child of the panel itself. you then have to drag-drop them onto the group and reposition them. If you do that for a multiselection of modulators, always make sure to hold down shift before left-click for dragging. Otherwise your multiselection will be lost and some of the modulators become invisible as they are positioned outside of the group bounds…
Another remark: I did not see much sense in implementing controls for the lower partial, because I don´t think one will have the need to control the upper and lower partial in realtime. As a sound editor, I would use my panel to edit the upper partial, save it and then assign it als lower partial if I want to. But that´s a matter of taste…