I won't sugarcoat it, almost every itch project I've seen do a (mostly) full reset over author displeasures with the narrative has without fail ran into loss of meaningful aspects from the original versions and often partial or complete abandonment.
This is usually due to the simple fact that making a game from scratch already comes with burnout naturally, but having to re-tread plot/systems ground you've already covered before? That makes the burnout a LOT worse because you no longer have that same pleasure of pioneering as much fully new content - I imagine you may have already noticed how exhausting it can be.
I REALLY don't want to see this project meet the same fate, keeping a careful balance of bringing back past systems and developing new systems to keep morale up is going to be a delicate balance but I truly wish you the best in keeping up with it. I can tell you have a lot of ideas and passion for this upcoming remake, and I can't wait to see what you come up with! But above all else, just make sure not to let yourself get overwhelmed and fall into the burnout spiral, because its so much harder with a re-write like this to escape it. A delay is much better than falling into that spiral.