First, we didn't change the content of the black chests or way the game allocates artifacts. Basically, the game keeps a list of the potential artifacts and checks them off as they're assigned. Chest contents are assigned when an area first spawns and whenever it respawns.So, if you enter an area with a black chest but don't open the chest before the area respawns then you lose the possibility to get the artifact that was assigned. That's not usually a problem with most black chests since the normal respawn time for an area is 600 days.
The notable exception is the Training Hall, which has a respawn of just 30 days. The developers mistakenly left that set to an instantaneous respawn. One can lose access to many artifacts by repeatedly re-entering THall and not opening the black chest, and that can happen more quickly in an official version of the game. The same principal probably holds true if the player has deleted minisaves for an area containing a black chest.
So, unless you've been playing in a peculiar manner, the only thing that would make sense is that the portion of the data table that tracks your assigned artifacts has become corrupt. Regardless of the cause, kkc can tell you where to find that data table and how to tweak it.
