simulation from schematic file

before you run NativeLink, you should remove commande.bdf from the project files, and make sure that commande.vhd is in the file list. then run Analysis and Elaboration, then run NativeLink RTL Simulation

as it is now, Quartus has not generated a ModelSim .do script that includes your converted commande.vhd file. in order for it to do that you have to run Analysis and Elaboration with the converted .vhd file as the top level of the project (and the .bdf has to be removed to avoid naming conflicts)

you may opt to use 2 QII project revisions to switch between .bdf and .vhd in your file lists