Boron in sufficient quantities will distrupt the activity of beneficial flora, yes.

Sufficient quantities is well above the amount reccommended for putting in your drinking water at beginner's levels, though. Deadly dose is at 2.66 g/kg for rats, and that's.. far above what one takes for combating flouridosis and candidiasis.

Boron will however make your skin feel dry if your sodium, calcium and potassium levels are low. It acts the same as magnesium in the body. It's a good idea to eat heavy on the fruit and veggie side of things to compliment the treatment.

Boron is a rich element in foods from areas where there's good levels of it in the soil. Apple trees and other fruit trees which originate from the middle east enjoy it for fighting off fungal infections. It's similar in the body, though especially in plants it's used for constructing strong cell walls.

In the case of gut flora, the boron water will most likely be absorbed from the beginning of your small intestine long before it reaches the 30 or so feet of the whole length. The first 3-5 feet of the small intestine in a healthy person is relatively sterile, because of constant release of bile and stomach acid when food stimulates it.

In other words, it will not disrupt gut flora living in the intestinal tract below the area where you absorb water. Excepting the case of what is living in your intercellular tissues around the bloodstream, and critters that like to live off your blood ( parasites who live in the intestinal tract and rely on candida for their survival), your gut-flora-garden is safe.

If you are fighting off symptoms caused by a leaky gut, then you're green-light on trying borax. In cases where intercellular infections (candida and the like) are heavy, it's important to reduce the beginner's dose by half or more and titrate up slower still. My first encounter with borax water as a type 1 diabetic had me peeing like a horse for 6 hours!

Boron is a keen little fighter against candida infections. :)