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With the new system, several people are editing gyms without knowing that it will disappear and are reappearing in places of private residence and not as it was before, as in parks and public places.
If a Wayspot has been moved away from its physical location, then you can file an appeal at https://community.wayfarer.nianticlabs.com/categories/location-edit including any photographic evidence and Google Maps/Street View links that shows the location of the object.
Yes, you can appeal or return it to its original with edit but when it returns it will not return to the gym if not as pokestop
You cannot protect anything currently xD