You've discovered a mighty complicated bug here, and I'm not entirely sure how to fix it. Essentially, I use three generic variables to move that event along once you've completed both options, but these same variables are in sparse usage for weapons and equipment.
I'm not sure what you specifically did to make this rare issue occur, but I wouldn't:
- Fish
- Use any T5/6 Armors
- Use Elemental Dancer
And I'll add another check in to make sure this bug can't happen again-- Sorry for your lost progress, try playing on "Story Mode" and holding W to skip through to get back in less than ten minutes flat.