I was able to return my previous state of game by removing access of the executable to the Documents folder, deleting the Endless Dungeon folder in Documents, then going to /Users/<username>/AppData/LocalLow/AMPLITUDE Studios/ENDLESS Dungeon/ then deleting the Player.log and renaming Player-prev.log to Player.log.
Upon reloading the game I was back to my previous level of progression (albeit still with the missing crypto key I was trying to fix).
I have windows protected folders enabled, including Documents. I was unaware that Endless Dungeon required access to Documents for save files because a) I did not see the notification asking for access/stating access was blocked, b) I had no problem with saves, meta progression, etc. I have loaded and closed the game multiple times since release day and completed a number of runs with a large amount of meta progression (all heroes unlocked, all districts unlocked, various hero chips bought, etc.)
While attempting to address my other reported bug (lost crypto key progression after quitting a co-op game) I realised that the game executable was requesting access to the Documents folder (to this point it had not placed an Endless Dungeon folder in Documents - it was missing entirely). I gave the game executable permission to access this Documents folder and then reloaded the game. Upon loading the game it was in a state where the introduction/prelude/tutorial was already completed, I was in the saloon as Zed, and ALL meta progression had been lost. Nothing at all was unlocked, it was like I had just bought the game and loaded it for the first time.