The vet didn't say not to soak (at least, not that was mentioned in this thread). It was just mentioned by members here because that is a common mistake to make when a BP is going into shed. Soaking is not helpful for the shedding process, and sometimes can make it more difficult.
I hadn't heard that about antibiotics and the kidneys, but it does make some sense. And if it comes down to a choice between making sure a medicated snake is as hydrated as possible...and risking a flaky shed...I'd risk the bad shed. A flaky shed doesn't hurt the animal at all..it's just not pretty.