Even if the water is not totally immersing the LECA, it will wick up to the soil (usually this is a good thing). If you are willing/able to move your frogs temporarily, you could remove as much water as possible from the LECA layer and keep the top open. But I've found that substrates such as coco fiber when its soaked takes a long time to dry...so not sure about the effectiveness of a few days worth of drying.
Is there a particular reason why you are concerned about the wet soil? Our auratus did fine while the tank was getting drier with time. To be honest they seemed to really enjoy the damp. Probably not the best conditions but they have done very well.