Oops, Sorry. I didn't notice you've moved to using .rpa archives. I just copied the contents into the existing folder. Haven't tried it yet, but my guess is that that's what caused this.
So, yeah. It was just a PEBKAC. What a way to make me feel like an inconsiderate idiot.
But regarding point C: I didn't do any edits in Crescendo, I just peeked into the code (I was actually looking at the old code, that's why I probably didn't see spot the error, but I did notice that notepad was sending me to an incorrect line when I told it to go to line 48. Also I should have spotted the CG and sprites missing. Or I should have spotted the .rpa files.). The edits I talked about were done with other VNs. As far as I remember it was fixing a typo in Blackgate's code on Gruff's route quite a while ago and trying to one up someone who used image editing software by doing a text edit in Minotaur Hotel - it was an edit of Asterion saying "There are very few things better than a good book.", they photoshopped it into "There are very few things better than a good dick.", I edited it into "There are very few things better than a good company throughout the day and a nice cuddle in bed at night." (You know: naughty, horny vs wholesome, romantic.)
Edit: Yep. It works. Now I feel like a total piece of trash for wasting your time.