You have to seal it, otherwise you'll lose air the AFM has already 'counted'.
Is there enough of that pipe to use a rubber stopper ? My catch can vent is put back into the intake pipe but it was done so I could take it out and vent it to atmosphere should I need to. They gave me a rubber plug, which is essentially the same sort of thing as you'd find on a cheap table leg. This would stay on with a hose clamp.
Not sure if that would work for you cos I can't picture how your bov looks like but it might give you an idea