I'm not even sure what those are exactly. Are singular flags secrets that don't trigger any other flags when they go off? Or rather, they must all be triggered singularly before they activate secrets? Gimme a brief description of how they work.
Even then, I'm still using the tried and true screen animation method by doing this. Singular flag, singular flag -> trigger to new screen. Scripting might otherwise let you simulate a vulnerable period where you get a few minutes to beat the crap out of the boss as fast as you can, registering hits until it recovers.