Ok. I went through the code and I have indeed made a mistake.Regarding Kyo this update.
My Cat was quite frosty with her when she went to see her about her promotion and talking to Ele later had her mention that Kyo was upset that Cat hadn't forgiven her. Cat said something along the lines of Kyo treating her so badly for so long and the excuse of she did it to make her stronger doesn't make it okay.
I have had Cat forgive her or take the lighthearted approach everytime when dealing with Kyo.
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So that should fix the problem. Now, one problem is that you would need to go back and do those scenes again. But if you would prefer, I can also do a cheat option or a button combination to change the flag.