So I confirmed the existance of the bug before started 2 new games that used the debug mirror and made a save of the progress. Now all my saves are receiving exp correctly, displaying both the total exp for each character increases, and the exp value to the next level decreases.
I'm certain that the total exp value displayed would decrease after each fight as i just assured myself a half hour ago, but now I'm unsure if the remaining exp display beneath it was or wasn't working properly previously. :/
I didnt get to check if i could go back down levels but I guess my weird problem is fixed now, and I now know a solution, despite not being able to fully locate the cause. ¯\_(••)_/¯ I believe strange interaction with the bed is involved because when I first came into contact with it, I interacted twice in a row by mistake (because I'd been farming herbs), turning it day again faster than it should have been able to.
If my problem couldn't be undone I planned on grinding for herbs in Hyuchi or Jack & William's cave and only participating boss fights to minimize exp loss, but now I don't have to. :)
Thank you Tiagox for reading my comment and informing me on how visual character disablement works. :)
The quantum table was a table model that you've (edit: mostly) progressed from using which filled a whole tile, existing on the edge of the Peccora mansions interior map, that I referred to in my first comment about 2 years ago. :)
You removed it in the update of the furnishings of Peccora mansion & removal of the invisible obstacle in the chapter 5 cutscene. It was a joke from quite a while ago. 😅