Hello François. In my case the surfaces were generated with CAT12, and I see on the GUI that it doesn't give me the option to project scouts from one subject to another using the path you mention.
If it helps, I'm basically trying to create a hybrid atlas combining some scouts native to the Desikan-Killiany atlas and some scouts from the Human Motor Atlas Template (HMAT), which I imported manually.
I have the same problem as the user above: I can create the hybrid atlas for one subject, but when I open it on the next subject I get a bunch of dots, due to the vertex indices not matching; as you explained.
So, what's the alternative to projecting across surfaces when the surfaces were generated with CAT12 or spm12? Could you point me in the right direction? Much appreciated.