My understanding is as follows-
400V battery is supposed to keep the 12V battery topped up with charge as required, in almost all circumstances and even when car is off, but if it doesn't do this then the best way to try force it to charge the 12V is to charge the 400V battery as you say, or else to drive for at least 20 minutes. There is a software update for EQS from around June I think (only available at dealer) that helps reduce draining the 12V possibly either from from leaving doors open, interior lights on etc or with the keys nearby that puts the car on high alert that doors may need to be opened - I don't know the specifics.
Best option is to contact Mercedes else you could leave the car charging at a slow charger and locked overnight, with keys a good distance away just in case, and if that doesn't help then contact Mercedes. Contact them anyway to check about the 12V software update. Be interested in a report back what works for you.