Can you save/load different input autoconfigs per game?

So i was trying to find a way to fix this problem

And the only way i managed to make the right analog behave properly without the big deadzone was to “transfer” the deadzone to the left stick. The way i did this was to change the input config via the RetroArch menu and not via the main/content menu. What i did was to swap the left and right analog controls.

Problem is that when i close the game and reopen it, it goes all default again. In order to avoid this i have to uncheck loading the autoconfig file. Or load a new one i assume. But if i do this isn’t it going to affect all games and cores? So is there a way to load a different autoconfig for the games where i need to play with the right stick?

Or, even better, is there a way to remove this dreaded deadzone from the right stick?