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Hey there; there is no good way as far as I know. But take a look at how TowerFall handled it with their Dark World expansion: https://mattmakesgames.itch.io/towerfall-dark-world

Essentially, they packaged the expansion files separately, put a big disclaimer on the expansion page that it's not stand-alone. Once purchased, there are instructions on how to apply the expansion to your existing Towerfall installation (basically just copy, paste, and overwrite some files).

Please consider releasing the DLC here and not making your itch.io consumers second class citizens. :)


(+2)

The problem is that the DLC is not separate files, it completely overrides the original game, importing the vanilla saves the first time you run it, but otherwise maintaining a separate branch from it. The only way to make it work is to make the base game a prerequisite for getting the dlc, which is what itch doesn't have.