What do you mean when you say that the main bacteria are “damaged”?
If human flora can change and adapt, why cannot it “reshape”, as you call it?
It is well known by medicine that long broad spectrum antibiotic rounds cause permanent and long lasting damage to the gut microbiota.
It is also well known those changes may compromise important dominant native species ( main enterotypes and phylotypes )
These species are human origin species acquired by a selective method in the first years of life. During life, there are “minor” changes in the flora composition influenced by the food, environment, medicines, etc.
When a mayor change occur as a result of antibiotic intake or any other offender, there isn’t way to recover it but with a massive bacterial transplantation from another healthy human. At least, this is the only way science has done it so far. Taking oral pharmaceutical probiotics or changing the alimentary regimen, isn’t possible to recover the balanced bacterial community needed in the colon.
This isn’t a secret and the reason because Fecal Transplants have emerged.