The salt water flushes simply run right through your stomach and intestines, by-passing the bladder, and running out your bum. It's basically like running a hose through you. Of course it doesn't get all the stuck stuck stuff off the sides of your intestines...but I'm sure that it does do *some* cleaning out.
The Bentonite and psyllium drinks suck toxins out and scrub out your intestines releasing old rubbery mucoid plaque. If you take the salt water flush while b&ping, the b&p won't work very well...it'll just get flushed out.
It is totally fine to leave the salt water flushes out, if you are b&ping.