Ah, okay. That would explain why I couldn't find them all. Still a lovely little game.
And I understand the intentional lock from a design perspective. It really fits well for the game's mood and theming, but goes a bit against my completionist desires xD So forgive me for cheating a bit.
And it means I still have to remove the ending saved data from AppData to play the fixed version.
In case anyone else is wanting to reset and look for the rest of the relics:
For me, in "...\AppData\Roaming\Godot\app_userdata\ScanBot and the last Mind" I had to delete the "final_desire.tres" file to reset the game.