
I don't know what sort of shoes you're using, but if they have breathable linings, then I assume the outer material is also breathable, in which case maybe it shouldn't be made waterproof afterwards.
I'm baffled by manufacturers who put breathable linings into footwear that needs to be waterproof on the outside. If they're waterproof, then where does the vapour from sweaty feet go? Well - it gets trapped between the breathable liner and the outer material, where presumably it can rot the material or stitching or whatever else is in there.
A lot of modern man-made materials don't need handling with kid gloves the way old quality leather did, nor do they always cost as much. So - maybe bung your footwear in the washing machine and dry them on top of a radiator if they'll stand that sort of treatment. Consult (or insult) the manufacturer if in doubt.