Hi Diego,
the information on identical masks built by DOMAINcfg with and without introducing a nest was meant to stress that masks are not updated using DOMAINcfg - my original post still holds.
I am using DOMAINcfg from NEMO 5.0 (tag). I also see the difference to NEMO 4.2.2 and thought the issue should be fixed - but it is not.
I now tried to find my way through the code and, although not 100% sure, now think, the issue is not with the timing of when mesh_mask.nc is written but of when tmask (and the other masks) are computed. To my understanding the respective routine is called before any update routine and the masks themselves are not altered later on.