Firstly, try not to think of height and speed as two separate things. Think of them as one thing = ENERGY the a/c only has so much energy it cant be gained once the engine has stopped.
With regards what to do with the flaps, its does come down to judgement. If it was me, I would retract them straight away (unless you were taking off) - you can always pop them back down. I never used to like using flaps when i was teaching, firstly because the flaps on the ac I was on were crap! but mostly bcoz there are better ways to manage energy. sideslipping is a great way of loosing energy, as you can be very precise about how much you lose. Another good way to loose height is not fly at the best glide speed (because its the best glide speed) have alook at the drag curve, youll see the faster you go, the more drag you produce.
If your in any further worries about whether you should re-track the flaps, think of it this way. If a certain BA pilot hadnt retracted the flaps on a 777 after the engines both quiet on him, lots of people (on and off the a/c) would have died