ph101, IMO you are fine leaving the water where it is and not worrying about the other 2". You will get a little wetter when plugging the rets and your blower will have to work a little harder to evacuate the lines (you also need to plug them while the air is comming out of them to insure that they remain dry).
1 other thing to worry about is the cover, if it is a safety cover - no problem, if a watertube cover - draining it too low will keep the cover from being able to float on the surface and it will fall in.
My computer is acting up right now, so i will end here - if you have any further ?s, post and they will be answered.