On the whole retracting flaps and experiencing an altitude loss.... isn't that mostly a butt feeling? Cause if managing the possible increased speed correctly, and being able to maintain the best glide throughout the retraction, there shouldn't be any loss of altitude?
On the other hand, in case of a headwind, it may be feasible to keep your speed a bit higher than best glide in order to reach a desired landing site, otherwise the better glide may be eaten up by the reduced speed over the ground.
Another one, which I've heard, but never tried though.... increased speed into the ground effect, and then using the ground effect to strech the glide can also be an option....