it really doesn't matter if you run a incubator dry. The whole idea is to get the humidity correct.
rules of thumb for humidity:
humidity is based on surface area and air speed. Water depth has no affect on humidity once the water temp is stable to the temp of the incubator.
molecules of water vapor are formed on the water surface before reaching a level where they will break the bond with the water and become airborne humidity (not very scientific way to explain it). The more water area the more molecules are trying to break the bond thus higher humidity. Now in your case the fan is assisting the molecules by blowing them of the water surface breaking the bond earlier then they would with no air flow.
So to reduce your humidity you need to make the water area smaller or reduce the air speed over the water. e.g put a small cup of water in the incubator rather than the large area the channels provide. (do not place the water where the fan blows directly over top of the water.
(another trick is to use a smaller power supply to the fan to slow it down and make it more of a mixing fan. If the fan is 12v use a 6-9v power supply)