I haven't had a normal calprotectin result ever during a flare before but I have recently had a normal calprotectin result and I still have symptoms - what's causing them I don't know and my doctors don't know either because all my scans look good so far.
On the one hand I do believe my doctors when they say there is no sign that I currently have active disease...but on the other hand the symptoms feel a lot like a flare up of active disease.
I think it might truly be hard to distinguish at times for the patient what is active disease and what are symptoms caused by other things (complications, or the potentially real and potentially not 'IBS' that some doctors will diagnose you with along with IBD, and all those other things that you always need to rule out) since our guts have only so many ways to act up.
This isn't exactly an answer to your question, except to say that I am wondering, along similar lines, whether this might be the case for me.