I tried to copy with mates in SW 2015 SP1.1 but when I try to add the new mate references, it says:
"These mate selections conflict with existing mates"
It seems like the new mates are using old references and they cannot "override" the old mate refs with the new mate refs. I say this because the new mates are surfaces that should be compatible with coincident and concentric.
Ok, we, (my VAR and I) fixed this issue by docking the mates window in the model tree area. Then we restarted solidworks and tried copy with mates again and it worked.