Synth_critical_pin

I am using Quartus II 9.1 on Windows. Looking through my Fit report file, I see some warnings regarding SYNTH_CRITICAL_PIN ignored on several pins relating to the PCI core (TRDY, STOP, DEVSEL, etc.) because of "pin not found." I run an up-front synthesis with Synplify Pro, and I wonder if that may reduce my pin names to another name so that this assignment does not find the pins as expected. I'm wondering what missing this SYNTH_CRITICAL_PIN will do. My PCI design works fine.

Thanks,

-Brad