No. It does not permanently change the eye health or the vision system. It is definitely a compromise, but it works very well for many people. If you are not doing as well as you hoped for, hang in there. It takes weeks or months for your brain to learn how to see with this system.
No, it will not cause your vision go worse. Most people choose monovision contacts when they have myopia and presbyopia at the same time. The dominant eye is used for distance vision while the other is for close vision. The only disadvantage is that monovision doesn't provide adequate near vision to give them the freedom from reading glasses they were hoping for.