The way it is managed in the legacy System: The GP registers a new diagnosis (foot infection or diabetic foot). The GP write the note associated to this NEW clinical problem.
NO CHANGE is applied to the longitudinal problem (Diabetes).
There is no such thing like relation between problems, but: The GP can mark more than one diagnosis associated to a clinical note. This way, you can retrieve the notes taken, with a diagnosis filter. So the information gathered in the infection foot process, would also be available on the Diabetes longitudinal problem (as long as the GP mark both diagnosis).
Of course, if on the job of building this new system, we can manage to offer a new feature that enables to link related problems that would be awesome .
By the way, I am glad to answer all the questions you need. In the end it is all about being sure we are correctly aligned in the understanding of the use case. Furthermore, it demonstrates your interest in helping by sharing experience and know how. I am very grateful.