So, this happens when the name of the bot in the DNA file (as put there when bot DNA is saved) does not match the name of the DNA file itself. Today, the DNA file name is used in the species structure to link bots to their species. Graph colors leverage this.
For now, I've simply removed the saving of the bot FName in the DNA file. Thus, whatever the DNA txt file is called when bot DNA is saved will be the bot species name if that bot is reintroduced. This avoids problems with colliding with the previous species.