I don't understand the issue.
 
As far as I know and can tell, there is only one place to put a website in CM-A, and it's on the main screen. The individual contacts have fields for Name, Position, Primary, Phone Number(s), Email(s), Misc Info* and Misc Date(s).
 
If you have a report that puts the website with each contact, then yes - deleting it from the only place would delete it from every place.

Yes, it is linked to the "Contact Account". Are you saying that if you enter a website there, that one website shows up on each Contact Account? And if you delete it there, all websites are empty?
 
If so, that is certainly not the way it's supposed to work... you have a major problem. What version are you on?