Hello!,
I'd like to hang my head in shame, and sincerely apologise for wasting your time.
I created a new airframe in Simbrief, recalled a flight plan in the Challenger, got the message that says "FPLN Loaded", looked at the Sec FPLN, and it's there (previously, i've been expecting it to just appear as the active flight plan).
Really sorry for wasting your time, it's been a few months since i've used X-Plane, so I'd forgotten that it loads the plan into the secondary flight plan.