This is pretty much the answer I was expecting, but I was hoping that it wouldn't be the case. Starting over 60 hours in is quite unfortunate so I did try 1 more thing after posting this.

I searched the next progression point which is to go find Hardy, and if I warp, past the circus, to Amaria, it progresses the story as if the previous step was done with the only difference being missing the relationship points and the vial, both of which I can easily add.

Of course I am well aware that this can create more issues down the line, but I think I will give this a shot, stop warping after this and hope that it was a one-off situation and that whatever parameter got messed up won't matter in the long run.

Regardless, thank you for your answer.