Organ stop scoring
Remember the question I asked on Music Stack Exchange the other day? Well it has bore answer-based fruit and provided more insight into scoring for organ.
The eventual answer also provided an example of an organ piece featuring a stop changing on held notes: in César Franck's Grande Pièce Symphonique the player is instructed to add reeds during a held chord (as demonstrated in the video below at around 3'54).
In this case the instruction to the performer is written: "Ajoutez successivement les jeux d'Anches à chaque clavier de facon à arriver graduellement au Grand-Choeur" (Google Translate) as found in a French version of the score, on page 3. It seems there are no hard and fast rules for such performance techniques however: a symbolic notation could be developed if the complexity of the part required it.
At the moment I'm thinking such a notation is probably not necessary. I'll understand this better though after I've had a session with the organ.