The first thing I would look into is if Lutris has permission to write in your Games folder. I’m running on the default ~/Games/ folder and it can definitely write config files there…
Just to confirm, you’re able to right click configure in Lutris’ menu and when you do it again, settings reset?
Since I installed Diablo 2 through Lutris in the default ~/Games/ folder it should have permission, right?
Yes, right click on Diablo 2 in Lutris --> Wine configuration --> Graphics --> check Emulate a desktop and set to 1280 x 960 --> apply. When I start the game next time it’s unchecked and reset to 800 x 600.