Dissappearance I/O pins after ECO (Quartus II)

Hi, all

I have some problems about simulation by third pirty tool (Mentor modelsim).

I use Quartus II for synthesis. After synthesis, some LCELL is added to the

design by ECO (not GUI, but original script).

Then, EDA Netlist Writer writes the netlist for simulation using ModelSim, however, all I/O pins disappear in the netlist for simulation. I wrote the I/O pins by hand, however, it doesn't work. Do you have any solution?