Thought I should share this as I have locked myself from being able to complete a puzzle. I’m about 20 hours in.
I was able to reset it by leaving the dungeon and therefore having all enemies respawn which I’m pretty sure was unintentional from the game devs.
To avoid spoilers as much as possible, I’ll just explain it this way: when you reach where Seraï is from >!eventually you’ll have to go to the sky base!<
There is one particular puzzle in there where you need to push 2 blocks from a higher platform down towards the center (and then push them around some more), but it’s possible to push them in the opposite direction from the start and have them land outside of the puzzle bounds and make them impossible to interact with again.
Here’s the image of that particular area: >!https://imgur.com/gallery/taKxgxy!<
Hoping this will save some from wasting as much time as I did.