It's easy to tweak values and such, but changing the genre would be a matter of art assets. You'd need to have an equivalent for every technology, building, race, overworld sprite, GUI element, and so on. You could recycle a fair bit of it, but most of the human buildings would have to go.
Looking at the game files, I'd say for a reskin to fantasy it'd be a job for an artist/writer team more than a coder, but that team would want to wait until game is balanced.
Ah, and just so you're aware, this isn't a traditional 4x. Converting it to be one would probably be harder than making one from scratch.
fake edit: drat, ninja'd by the guy making the game.
What he said.