Yes, naming changes have been made to the underlying transceiver Megawizard files in Quartus® II 12.1.
Previous to Quartus® II 12.1, an example name might be:
<transceiver instance name>/stratixv_hssi_10g_tx_pcs_rbc.sv
In Quartus® II 12.1, this would change to:
<transceiver instance name>/sv_hssi_10g_tx_pcs_rbc.sv.
These name changes could cause your .qsf assignments and/or .sdc constraints to be ignored during compilation.
Once you have regenerated your Stratix® V transceiver instances in Quartus® II 12.1, you should then correct your .qsf and .sdc files by performing the following global string replacement:
replace:
\'stratixv_hssi\'
With:
\'sv_hssi\'