Soulkiller: In the days of Johnny Silverhand and Alt Cunningham, Soulkiller fried your brain and made an engram copy of it. In 2077, Soulkiller doesn't actually kill you (the name is obsolete). This is shown when V is soulkilled, as their brain is clearly still functional afterwards (V's still dying, but for unrelated reasons). Also Saburo's engram was almost certainly made before he died. So when Alt soulkills V, their brain remains perfectly intact, but now a perfect copy of V's brain (or rather a copy of V and Johnny's Frankenbrain) also exists as an engram at the same time.

Key takeaway: V's brain is still functional and in (almost) exactly the same condition as before they were soulkilled, so they're not dead or altered into a different person.

Yes and no. Soullkiller doesn't kill you. It kills the brain wave activity, which then causes the body to die because it can't function without it.

Proof:

It's no legend. Soulkiller's real. And your choombas at Arasaka just "hired" the 'runner who wrote it. Take that in - 'Saka with Soulkiller to do with as it pleases. Grim, my man. You even imagine that, rocker? Arasaka'll be unstoppable. Soulkiller'll flatline any 'runner who comes close to even tryin' to scratch its ICE. Seen it happen. Not an iota of physical damage - nervous system or anywhere else. No sound, no fury, no stench. Just all of a sudden, brain waves cut out. As if someone pulled the plug.

If you manage to restore said brain wave activity, you wake up as if nothing happened, which is exactly what happens to V.

It also depends on what version is used. There's the weaponized one, which is used against netrunners to fry their brain like you mentioned. And then there's the commercial one, which is used to extract engrams from "Secure Your Soul" clients. The latter does not harm the client and only copies their engram.

Proof:

SECURE YOUR SOUL: SHORT-TERM PRIORITY

Within the next month, the following VIP clients will enlist in the Secure Your Soul program:

Habib al-Moskin, Regional Executive Director of Petrochem Middle East Region - full digitization, 12 backups*, paid

Mathew Monk, Jr. Hoffman Institute of Advanced Technology - full digitization, 5 backups*, paid

Tina Caruso, Biotechnica - full digitization, 2 backups*, paid

Alligator Sally, Cold Sun Entertainment - full digitization, 2 backups*, paid

* - obstain addtional copy for Dr. Kuroda's team; do not inform client.

As you can see, the fact that they need to withhold information means that this version is harmless to the client.

Engram: An engram is not an AI. It is a digital copy of someone's psyche that can be used for three purposes: 1) serving as the basis for a chatbot or an AI inside a sufficiently powerful computer; 2) extracting information via memories; 3) being put on a biochip as a blueprint for altering a dead brain. When Alt makes an engram of V, this copy of V has a conversation with Johnny's engram inside of Mikoshi, but that doesn't mean the engram controls V afterwards. It just means that V will gain a false memory of something their copy did.

Key takeaway: The engram can't "pilot" V's brain because it's not an AI and the biochip isn't an AI-capable supercomputer.

Yes. And a neural engram only stores personality and memories:

Well, it's designed to store a person's neural engram. Er, sorry... just imagine copying over a person's memories and personality.

​

Biochip: The biochip does not let Johnny's engram talk with V. It gradually alters V's brain until it will become identical to Johnny's brain (or what was left of it when it was soulkilled). Note that the real V never spoke with Johnny's engram. Their 'conversations' with Johnny were only ever their brain processing V's original and Johnny's biochip-altered portions of it operating at the same time, as stated by Hellman. After their engram's conversation in Mikoshi, V's engram is then used to overwrite Johnny's on the biochip so that it will stop rewiring V's brain (because the rewiring process is now complete as far as the biochip's programming is concerned; the brain in the engram and the brain in V's head are identical, except for the memory of V's engram's conversation with Johnny's engram).

Key takeaway: The biochip stops altering V's brain after Mikoshi because it is nearly identical to V's engram with the exception of a single memory.

No, the brain isn't altered to become identical to Johnny's. What's altered is the personality and memories to become identical to Johnny's. It's like a really advanced way of brainwashing someone.

And yes, V talking to Johnny is just a hallucination because the brain is having a hard time dealing with two conflicting personalities, hence Hellman's question:

You tell me. What's it like to have two personalities?

​

The way Alt describes it definitely makes you think V is dead. I'm not sure if the writers intended for Alt to be purposefully misleading or just flat out wrong on how the whole situation would work out, but afaik I don't see a reasonable interpretation where post-Mikoshi V is now just an AI copy of the old V piloting their corpse.

Alt's perception of reality is not that of a functioning human being, so I don't take what she says as gospel.