Well....
I am subject to someone with more wisdom than I coming along to correct me, or overlay my thoughts with more detail, and further subject to a qualified flying instructor (which I am not), presenting accepted training techniques, but...
So far in my flying career, I have come to accept that if you are gliding for the purpose of best glide ratio, you want the greatest L/D. If you extend flaps, you upset that ratio. Once upset, you can't just put it back as before, without a loss. The loss is the setting with the loss of lift, and the need to loose altitude to do a power off acceleration, to restore the aircraft to the flaps up best glide speed. I suspect that the net effect of these losses would exceed any benefit resulting from the reduced drag of the flaps being retracted.
Though my only "proof" is the absence of something, I've got to say that if retracting the flaps for any phase of a landing between their first application, and wheels on the ground were necessary, or otherwise a good idea, a flight manual somewhere would say so. Aside from basic techniques, flight manuals generally present all of the information and techniques required to fly the aircraft. If it's not in there, you don't need to do it, and their probably is no beneift to doing it. I agree that there are some handling techniques which go beyond (like lifting one float out of the water on takeoff), which may not be mentioned in a flight manual, which are described in training manuals, but modulating flaps on approach is not one of them. You don't see airliners doing it, and they fly by the same physics we do!
In part, I would imagine that this no mention in training manuals is becasue of the dramatic differences in aircraft handling with flaps from one type to another - you cannot generalize this. I assure you that if you go from full to half flap in a gliding Twin Otter, you will need a lot of altitude under you!
So, certainly, as a part of becoming a proficient pilot at altitude, experiment with flaps settings. At altitude, it's not dangerous, it just has no benefit. I suspect that if you measure performance, you'll see what I mean. But if you really need to glide, use the flaps the way the flight manual says to!