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> I wonder whether its possible to transplant the bacteria out before such a treatment and introduce them again later..

In theory yes, but there is the challenge of avoiding re-infection with the one species you're being treated to eliminate.

Is the gut usually the main target or just as byproduct getting wiped? If not then its not necessarily an issue.

The target species may not be thriving in your gut, if the location of the infection you're treating is elsewhere, but it is probably present.