This is my biome config:

Tweaker.setScriptStage("BIOME_REGISTRY")
Tweaker.createBiome("moon_flats", "minecraft:plains")

moon_flats = forBiomes("biometweaker:moon_flats")
others = forAllBiomesExcept(moon_flats)

moon_flats.registerGenBlockRep("minecraft:water", "minecraft:air")
moon_flats.removeDecoration("CACTUS")
moon_flats.removeDecoration("DEAD_BUSH")
moon_flats.removeDecoration("DESERT_WELL")
moon_flats.removeDecoration("FLOWERS")
moon_flats.removeDecoration("FOSSIL")
moon_flats.removeDecoration("GRASS")
moon_flats.removeDecoration("LAKE_LAVA")
moon_flats.removeDecoration("LAKE_WATER")
moon_flats.removeDecoration("TREE")
moon_flats.removeFeature("LAKE")
moon_flats.removeFeature("LAVA")

moon_flats.set("name", "Moon Flats")
moon_flats.set("topBlock", "contenttweaker:electron_matter")
moon_flats.set("fillerBlock", "contenttweaker:proton_matter")
moon_flats.set("skyColor", 16772324)
moon_flats.set("fogColor", 16772324)
moon_flats.set("grassColor", 9470285)
moon_flats.set("foliageColor", 9470285)
moon_flats.set("enableRain", false)
moon_flats.set("GRASSPERCHUNK", 0)
moon_flats.set("genVillages", false)
moon_flats.set("genStrongholds", false)

moon_flats.removeAllSpawns("CREATURE")
moon_flats.removeAllSpawns("MONSTER")
moon_flats.removeAllSpawns("AMBIENT")
moon_flats.removeAllSpawns("WATER_CREATURE")

moon_flats.registerGenBlockRep("minecraft:stone", contenttweaker:moon_regolith)

moon_flats.addActualFillerBlock("contenttweaker:moon_regolith")

The stone doesn't get replaced with contenttweaker:moon_regolith.

moon_flats.registerGenBlockRep("minecraft:stone", contenttweaker:moon_regolith)

You forgot the quotation marks around contenttweaker:moon_regolith

I tried fixing that, it still doesn't work.

Where should I put this?

Anywhere before

moon_flats.registerGenBlockRep("minecraft:stone", contenttweaker:moon_regolith)

moon_flats.addActualFillerBlock("contenttweaker:moon_regolith")

should work. Personally, I have it just after all my Tweaker.createBiome(). It might also help to put the stone replacement in before the topBlock and fillerBlock changes.

Thanks, I'll try.

Try setting
Tweaker.setPlacementStage("BIOME_BLOCKS")

I know scripts are supposed to default to that, but sometimes it helps to explicitly set it.

I just loaded up your script, replacing the contenttweaker blocks with a couple I already had made, and it worked fine. You're problem seems to lie elsewhere. The two most likely problems that I can think of off hand are either

A) Your content tweaker blocks are not registered the way you think they are. I assume the topBlock is properly coming out as "contenttweaker:electron_matter"; if so, try replacing stone with that.

B) Whatever mod you are using to create your "moon" dimension is populating blocks in a way that BiomeTweaker can't catch the stone. I know that Lost Cities' "cavern" world type does this.

Sorry for the long silence. I've finally come around to working on the biomes of my pack again, and it still doesn't seem to work.

These are my biome scripts:

Moon Flats:
https://hastebin.com/gifekuviso.cpp

Moon Hills:
https://hastebin.com/uvehikaqip.cpp

(Note that contenttweaker:electron_matter is just a placeholder, it's easy for me to see if the script has worked. I'll replace it with something that makes more sense on the moon like moon_surface_rock or something once I manage to get it working. Unfortunately that's not the case.)

contenttweaker:electron_matter loads just fine. Here's the proof: https://i.imgur.com/0JcEWjq.png

I am using Advanced Rocketry to generate the dimension. This is how the dimension looks: https://i.imgur.com/KEchJa8.png

contenttweaker:electron_matter loads just fine. Here's the proof: https://i.imgur.com/0JcEWjq.png

Is contenttweaker:moon_regolith loading fine?
Did you try replacing stone with contenttweaker:electron_matter?

I can't get AR to load, so I can't really comment on whether that's the problem or not.

I'm closing this for lack of a response. You can respond even though the issue if closed if you want to pursue this further.