Fully fixed in 1.4 (no key is used more than once).
Partly fixed in 1.3 (the Chuxen hub has been removed so this specific instance is not an issue any more).
If the player collects certain keys but does not immediately use them in that particular map, leaves and visits other areas, picks up keys with the same name, and uses them in other maps, the first keys collected will no longer exist. This seems to be caused by different game maps using the same keys, i.e. the Castle Key.
This happened to me in The Canyon map, which is a major intersection that leads to four different quests. I had collected the Cave Key but did not use it to unlock that particular door in The Canyon map. I decided I didn’t have to open the path to Chuxen yet because I would save that for towards the endgame, due to it being a lengthy quest. I left the area to do some other quests, at least one of which also used a Cave Key. When I came back to The Canyon, I no longer had the Cave Key, and could not unlock the door on that map. This effectively prevented me from doing the Chuxen quest.
I’m wondering if this issue could be avoided by using uniquely named keys for each map, and keeping them in the player’s inventory for the entirety of the game. After all, a feature of this mod is that every dungeon allows the player to back out and leave if things prove too difficult.