I answered in a rush earlier and it might not really be a thing many people know. But you can change mod settings from main menu and it will then restart the game. When loading the game it may ask if you want to sync mod settings to your save, say no to that and it will play with the new settings.
So with this you can change even fundamental things like RSO's worldgen settings that will effect your ongoing save. Of course that could cause oddities on newly generated chunks, like suddenly changing map seed. But it's harmless for many other things. If you change stack sizes then something unexpected might happen like chest exploding items on ground, but i'm unsure and it depends on what you change.