ZDoom

It's all or nothing, i.e. either every flag stored in [b]dmflags2[/b] CVAR will be saved or none.
Actually, this CVAR is not changed indirectly, so saving it won't have undesired side effects.
Probably it's still worth doing something with [b]dmflags[/b] (without 2) to save both CVARs.

I myself am mostly interested in sv_dontcheckammo.

At the moment [b]dmflags[/b] and [b]dmflags2[/b] CVARs are not saved to config. Making them archived and no-init-call will solve this.
I guess one of the reasons to keep them permanent is [url=https://github.com/coelckers/gzdoom/blob/751e318c4e85fd91e965e42ca75b708f70114ab8/src/d_main.cpp#L2126-L2148]other commands line options[/url] that use these CVARs.
Searching through codebase reveals other places where they can be altered indirectly.

Now some Gameplay options CVars from ( https://zdoom.org/wiki/CVARs:Configuration ) are not saved in the .ini after GZDoom is restarted. So they only take effect until player quits the game. After player runs GZDoom again, player needs to set up this options again.

It would be nice for these CVars be saved in ini, so player doesn't have to set up them again on each game start.

I checked sv_dontcheckammo, sv_fastmonsters, sv_noautomap, sv_noautoaim. They are not saved.

GZDoom g3.3.2 - 2018-04-12 21:44:48 +0200 - SDL version