You're right, but I'd go with "the secondary control is ignored and clearly marked as such" ("ignored" light turns on or something). But yeah, if they aren't linked, there's not much you can do that will make sense.
Nah, the right way to compute the final inputs in a case like this is, "This design is stupid and is going to get somebody killed. There is nothing I can do at this level to fix it. You must physically link the two controls."