In "Threshold" achieving warp ten caused Janeway and Paris to 'evolve' into salamander-type humans, but once back on Voyager
the EMH was able to cure them of their odd affliction.
So why didn't they make the modifications to the warp core and get back to Earth at the end of the episode? The condition obviously wasn't life-threatening and could easily be reversed--which the EMH could do the moment they dropped out of warp in the Sol System seeing as he wouldn't be affected by the process.
So why not go ahead and do it then put up with the bizarre side effects for a few days?