There was an Lorekeeper interview about this in September with Steve Danuser about this. Below is his exact answer to it.
"This is a complicated question. How do you deal with things like alternate Draenor? There was a Draka there. What is that Draka? Is she alive? Is she dead? Is she related to the Draka in Shadowlands that we see? Or is there another Draka? We know that in Warlords of Draenor, Velen of that universe died. Does that mean there is a Velen in the Shadowlands? But what about the Velen in Azeroth? All these things are very complicated questions.
The way I would have you think about it is think of a rope… If you look at a rope, it is one thing, right? It’s something that you can grab onto, you can hold it, you can see it; think of that as a character. Think of that rope as Draka or Velen.
If you look at that rope more closely, you can see there are different threads that make up the rope. There are different twines that pull together, and you can pull off one of these threads if you want. But it’s still a rope, and each of those threads you can think of as one of the realities of the character, one of the streams of time… There is a thread that is the Draka from Draenor we visited in the Warlords of Draenor. There is another thread that is Draka on Azeroth as we know her… And there are many other threads that could be other realities that we never peered into. But all of those threads at some time come together to make that rope. And remember also that, as you’ll see, that there are many characters in the Shadowlands when they refer to time, they usually say that time is not a construct of Death. Time and Death are not related. Death is about eternity, not linear time. The manner in which these threads come together, that can take a very long time from mortal perceptions. Those threads can be separated for a time, but sooner or later, they do combine to make one rope that is that character. You can think of it as the threads of that rope, all the individual threads, are just waiting. And over time, they will come together but they can exist as separate entities for a time. That still doesn’t change the fact that they are part of one rope."
Thus one Shadowlands, with AU Ner’zhul becoming a thread within MU Ner’zhul’s rope. And because Death is about eternity and not linear time, when AU Velen died he became apart of MU Velen’s rope, joining the main soul in the afterlife, even though MU Velen is currently still alive.
Though it is currently unknown exactly how souls within alternative timeways that don’t exist within the main timeway, such as Uther Menethil*, or those from an alternative timeline making their home in the main timeway, such as Overlord Geya’rah, function in this system.
*Uther Menethil was from the time way Thrall visited in the Twilight of the Aspects novel.