Do you mean the files belonging to the XAMPP installation or the files belonging to the webserver that came with Mac OS X?
If you meant the XAMPP installation:
1. Stop XAMPP.
2. Set the files back. If you've not enough rights to do this, you probably get a warning that you are not allowed to modify the files. Is there a button 'Authenticate' available? If so, click on it and fill in username and password of an adminstrator account of your Mac. If the button does not appear, change the permissions of the etc-folder (File-menu > Get Info, section Sharing & Permissions) and give your self read & write permissions. Repeat this for every file you want to overwrite if you still can't overwrite the files.
Alternatively you can choose for 'Apply on enclosed items' by the etc-folder (click on the wheel icon in the Get Info window in the section Sharing & Permissions), but I'm not sure if this breaks something.
3. Start XAMPP.
I'm not sure if other files get modified after changing configurations in the etc-folder, but I think you won't get problems with that. It depends on how much your websites relies on particular settings.