I think a stab is different from cutting a part off/out of the body, in that the life fibers could just "stitch" themselves back together, like when you fix a hole in your pants or shirt or something, but if you actually cut a part out it can't create a new part to replace it. It seems to be implied, especially by Raygo saying she can come back unless her threads are totally severed, that the life fibers don't REGENERATE, they just stitch themselves together. Note when Raygo's hand was cut off: she didn't grow a new one, she stuck it back on the stump and it got fixed. Same with her head.
So basically, Nui probably has physically lost the eye, but if she found it again and stuck it in the socket it would probably heal up. It could also be that the life fibers healed her socket together and she wouldn't be able to fit the eye in, but eh.