On reading the linked legal documents [0][1], it seems that the CEO is trying to make the case that the CTO is focusing on CopperheadOS in a development role, rather than looking at it as a product. I don't know if that's true or not, but I could see why it would lead to this conflict.
However, I'm curious how Copperhead the company can send these letters demanding that the 50% co-owner do this or that. As equal owner, couldn't he respond to these letters by asking the company lawyers to send a letter back to the CEO making similar demands? Is the CEO "more in control" than the CTO because CEO is a higher position, even though they're equal partners?