I don't fly F27s or anything nearly that big, but here's what, besides the owner's manual, I would look at in considering whether flaps should be retracted for braking.
The aircraft is stopped by two things, drag of air against the airframe, and friction of wheels against pavement. Drag is dependent on the shape of the plane and the airspeed. Friction is dependent on the coefficient of friction between the tyres and the runway surface, on the area of the tyre in contact with the runway, and on the weight resting on those tyres.
On most types, retracting flaps decreases aerodynamic drag and increases the weight on the wheels. The question is, do the flaps add more drag or more lift: which effect dominates at rollout speeds? If the manufacturer specifies use of flaps for a short field take-off, doesn't that mean that right up to climb-out speed that amount of flap is giving more lift than drag?
Well, if the braking efficiency were really poor (imagine a runway friction index of zero), then the weight on the wheels would be irrelevant and the contribution from drag would be the only thing stopping the plane. (Responses to pilots' prayers I will assume to be unaffected by flap setting).
If the aircraft is a millimetre over the runway with full flaps, just above Vso, then there is no weight on the wheels, and the brakes will be useless until the aircraft stops flying. In this situation, dumping the flaps will result in the wheels hitting the ground, and the aircraft will slow down much more quickly than it does while floating.
Somewhere between these two extremes is your aircraft. Because drag increases with speed more than lift does, I suspect that the only aircraft that shouldn't have flaps up for max braking are those with very similar flaps up and flaps down stall speeds.
I go by the manual. I know the manufacturer picked the method of braking that allowed them to boast the shortest landing distance, so I'm counting on that being the one most likely to keep me on the runway.