I never thought to test this as I just assumed the extra drag would be the dominant factor, but you are right (at least for beta 4).
Light weight (56%), Full brakes, FULL FLAPS, Airbrakes retracted: 46, 47, 47
Light weight (56%), Full brakes, NO FLAPS, Airbrakes retracted: 45,45
Heavy weight (87%), Full brakes, FULL FLAPS, Airbrakes retracted: 35, 35, 34, 35
Heavy weight (87%), Full brakes, NO FLAPS , Airbrakes retracted: 30 ,31
So retracting flaps does reduce stopping distance. Though as Effte points out, this may not be worth the extra pilot workload. Interestingly (Read: this goes against my hypothesis) the effect was only minimal at low weight. Perhaps a tipping point was crossed at high weight that was not crossed at low weight? Or perhaps I am just plain wrong.
Taken together, this just strengthens the consensus which I beleive Effte, Yo-Yo and myself are reaching. A/S and skidding factors may need tweaking.
@mvsgas
As per PheonixBvo's answer.
You raised a good point about mentioning the A/P. All tests were done at Gudauta with a quick test at Kobuleti to confirm the results. Different (beta) surface factors will totally change these results. I should have mentioned this.