Wearing headphones will not reshape the skull inside your head. If you feel your skull changing you should see a doctor because something might be wrong with your head. What can happen, is a temporary phenomenon, when you use your headphones for too long, it can mark your skin above your skull because the pressure of the gear it's too hight.
Known player like Tyler1 or TimTheTatman talked a lot about this theme in a funny way.
It can happen, especially with headphones that use metal rims and they press tight you skull. Even with that dents or marks will heal up really fast because when you take it off the blood will flow normally. If that is your case please consider buying a new par of headphones, preferable more loose!
A good alternative is ear-fitting headphones, this ones are very small headphones that are fitted directly in the outer ear. Something like this will prevent the blood of your skin to be under pressure!
Not all hears are equal please select something that feels more comfortable for you own body!