What exactly do you mean by a 'clean' one? I've tried removing the mod info in the MyGameName.lsb file via lstools which leads to an incompatible save file.
Create a new modded game
Play
Save it as "ModdedGame"
Go to main menu
Go to mods
Deselect all mods
Create a new game, this one will be non-modded
Save it as "NonModdedGame"
Quit game
Go to /MyDoc/Larian/DOS/PlayerProfiles/YourName/Savegames
Overwrite this file:
* ModdedGame/ModdedGGame.lsb
with this file:
* NonModdedGame/NonModdedGame.lsb
At this point, your savegame named "ModdedGGame" has no more dependency. Your can even remove the files from your Divinity installation
May I ask what is this lstools you're talking about? It seams interesting.