PlanAhead shows the following critical warning messages when implementing my design:
The Design has a number of pads (IBUF/OBUFT) that have PULLUP/PULLDOWN components instantiated on their wires.
PlanAhead shows PULLUP/PULLDOWN components as unknown components.
After implementation the LOC constraints are removed from the netlist file (in the PAR NCD file).
To work around this issue, remove the PULLUP/PULLDOWN instance in the HDL file and give the PULLUP/PULLDOWN constraint in the UCF on the particular net.
This issue has been fixed in PlanAhead 13.3.