godstones

I'm watching little clips of additional notes and such on YouTube and one room that was just shown had the Transmuter in it, and I do not ever remember going in this room. Is there any other way to make the red godstone? I seriously had no recollection of being in the room with the incubating homunculi but you have to make it red to get to the forest. Or can you solve the balancing puzzle with the white godstone?

Did I just forget I had been there?

[Everybody's happy nowadays]