>> probiotics are likely to become less effective as the weak bad bacteria are killed
>> off and are progressively replaced by more resistant ones

I can't say I have a particularly well informed opinion on that possibility. I mean.. well.. it makes sense to me that this could happen. I can imagine one possibility of how this could occur : unfriendly microbes eventually adapt their arsenal of toxins and learn via selection how best to kill off the new competition. That is to say they learn and adapt to the new probiotic and try to kill it off in order to maintain their food supply. Just a theory.

Think of penicillin as an example and how it produces chemicals that kill off competing microbes, which we then make use of as an antibiotic. However these offending bugs in our guts are also likely to produce toxins that are much more toxic to our cells than penicillin..

We select antibiotics based on the fact that kills everything else, and spares the human cells to a greater degree (by this I mean we would have rejected it as an antibiotic if it proved too toxic to humans).

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"Some men, in truth, live that they may eat, as the irrational creatures, 'whose life is their belly, and nothing else.' But the Instructor enjoins us to eat that we may live." -- Clement of Alexandria (about 200 AD)