Yes, the antibiotic-resistant bacteria would pass on resistance traits to all the bacteria that repopulate the intestinal tract. There will still be some susceptibility as each new generation of bacteria will have mutations, but overall, the same antibiotics will be less effective.
It's' been known since the invention of antibiotics, that using them eventually leads to not being able to use them due to the development of resistance.
There are other issues as well, as antibiotics damage our DNA, mitochondria, and alter fats and proteins, which leads to mutations within our own cells.