Anyone who has played NetHack knows the gist: you're doing unusually well with some decent equipment and having just obtained Excalibur only to get swarmed to death by ants. Cursing your luck, you decide to keep on playing Dwarven Valkyrie and start the next run before seeing your old stuff...and the ants who killed you...and the sadistic ghost of your old character.
Had you somehow made it, you might have noticed that the sword of your old character isn't Excalibur, but your current one somehow is. What force is preventing you from now having two Excaliburs? The answer, my good friend, is the fundamental nature of the dungeon.
A bones file is almost always a very recent occurence when the player arrives there, with an essentially identical population, even if you've been playing for much longer or shorter than when you last died. Yet its place in the dungeon is basically completely different, with no preceeding or succeeding layers beyond an absurd coincidence. The simplest possible way to explain this is to assume that time and space operate differently within the dungeon.
However, the intersection of timelines is even deeper than that! Artifacts are taken from all over the fantasy classics, which asks the question of how Tolkien and Micheal Morcock's literature could remotely happen in the same pasts filled with destructive relics and dying decadent races. The temporal mix-and-match must stretch across much more timelines than just the ones a player can start with.
Many artifacts, in addition to possessing unique powers, also have alignments of their own. Almost as if they have a soul. This inherent uniqueness must be the reason why bringing into a level will displace the essence of the other.
Another thing to note is how Bones interacts with temples, yes, it would make sense that the NetHack setting has pantheons of Law, Chaos and Neutrality. But then why name the priests "Priest of [Deity]" instead of "Priest of [Alignment]"? Obviously the player's god has the same transcendant identity-nature as an artifact, except that their essence can enter much more than just one physical host. It doesn't matter if they're a messaianic pale serpent or a sun goddess or the opposite sex clone of the thunder god, what's more important is that Quetzalcoatl/Ameratsu/Athena represents Law.