I have one idea but i am looking for the solution for below scenario.
When ever i replace any component with new component it will ask for new references because the identity of the face or edge involving in the mate have unique identity for that part. Is there any way we can copy and assign that identity to the another face or edge of another component so that replace component option goes smooth for 100's of assemblies?
There is no automatic method, but it can be done manuall by synchronizing the names of the faces, edges, etc, used in the Mate Reference.
Entity Property
http://help.solidworks.com/2011/English/solidworks/sldworks/legacyhelp/sldworks/parts/hidd_ent_property.htm
Replace Component
hhttp://help.solidworks.com/2011/English/solidworks/sldworks/legacyhelp/sldworks/assem_1/hidd_dve_replace_comps.htm