This is a Fallout blog, not a Borderlands one, but I gotta answer this one!
It’s simple. New-U isn’t canon to the setting. It’s simply there to provide an excuse for things like checkpoints and respawning.
"That’s stupid!" you say? Well, you’re not alone. The writers have given themselves hell over this as much as the players have, because it breaks immersion, and is not helped by there being a damn quest in the sequel where you’re ASKED to use this very same system, BY THE MAN WHO WANTS YOU DEAD, to kill yourself. And he then respawns you normally after that. And doesn’t use it on himself in the finale.
I love Fallout, but things like that prevent me from saying the same about the Borderlands series, for which I merely “like a lot”, because, for all the world building, there’s some glaringly huge holes in it, like the New-U stations. If they had simply not acknowledged their presence in the game world, then all of this could have been avoided.
And yes, these things not being canon is official policy. You can “have fun” making up all sorts of excuses for why so-and-so character isn’t revived after being killed if they DO exist, but it’s just an even bigger mess if you do that.
Interestingly, Final Fantasy handled this same problem better, even though it’s seventh outing was infamous for failing to do it right. Ya see, in both the fourth and fifth games, there’s point(s) where character(s) sacrifice themselves to save the rest of the party. And in both games, you can attempt to use healing magic to bring them back, to no avail. In the fifth’s case, they literally use every spell & item in the book! But at least they TRIED!
The only way to justify a particular famous death in Final Fantasy VII is if you either go with “well, your characters never actually die, they just get knocked out” OR “there was something about the bad guy’s sword or the target’s genetic status that made her unrevivable”.
But neither of those things excuses the party for not even trying to save her, unlike in the previous two games of the same damn series! Borderlands, particularly the sequel, suffers from that problem, multiple times, when they certainly should have known better.
Just one of many reasons to actually be excited about Telltale writing a game in the ‘verse. They’re much better at actually writing stories, and they have a lot of experience using the franchises of others well.
Note: It’s not bad for a game to have stuff within it which doesn’t mesh 100% with the story. It IS, however, a very serious problem when that same system is acknowledged on one hand, and dismissed with the other.