If you want to edit a part of a reference, you can use the Set Reference Clip Mask tool with the Merge Mask Contents check box turned on. When you create a clip mask with this check box turned on, the masked elements are copied into the master file. You can edit the elements within the mask. The copied elements are grouped as a named group, which can be managed from the Named Groups dialog. Deleting the named group will just remove it from the Named Groups dialog, but will not delete the mask or the masked elements.