Another question though, say someones gut climate is not so hot, so let's say 2500 strains of beneficial bacteria are not in decent enough numbers to be of help...
Will those species completely die out eventually? Or if we can change the climate, will their numbers return?
You will never kill off all the beneficial flora in the intestines. There will always be survivors. These survivors can be stimulated to grow again with prebiotics. In general I prefer probiotics as a "jump start" after antibiotic therapy, while prebiotics are the best for the long run to increase the numbers of all the flora.
Then by consuming raw sauerkraut or kefir, and prebiotics, is it plausible to think a healthy equilibrium could return?
Yes, but again these are probiotic sources so they are great for quickly increasing the numbers of some strains. But these and the previous survivors still need to be fed on a regular basis with prebiotics to support all their growth.