I don't think that it stays resident. It passes through and does not populate permanently.
There are some things which can kill the bacteria but the spores are far more resistant.
I think that your problems are more of a consequence and maybe due to other issues and not because of the BS staying resident.
My reading on BS suggest that it can cause the break up of biofilms by what they produce. They are meant to produce tiny amounts of D- amino acids and enzymes which can together cause break up of biofilms. That is a reason why they are used in the probiotic supplements made for GAPS.