Simulation and models are not real. Maybe some "attacks" could be developed against a simulated mind, but are they due to the mind itself or the underlying infrastructure? Just because you can simulate a warp drive in software doesn't mean you can build a FTL ship.
In the case of a warp drive we care about a physical result (FTL travel), not a computational result.
We already have emulators and virtual machines for lots of old hardware and software. If I play a Super Nintendo game on my laptop, it's accurately emulating an SNES. The software doesn't care that the original hardware is long gone. The computational result is the same (or close enough to not matter for my purposes). If brain emulations are possible, then running old snapshots in deceptive virtual environments is possible. That would allow for all of the "attacks" described in this piece of fiction.
There are many bugs emulator developers (game console ans otherwise) have faced because of undocumented or emergent properties of the original hardware. Some games required those properties to function.
Yes sometimes emulators have bugs, but they do a good enough job that most people aren't willing to go to the trouble of using the original hardware. Also emulators can unlock new capabilities such as better graphics.[1]
Human brains are far more resilient than software, so my guess is that emulated brains won't have brittle corner-case bugs like emulated software. People today do all kinds of crazy stuff to their brains and remain functioning: drugs, sleep deprivation, getting hit in the head, fasting, aging, etc. If subtle changes to our brains could cause our minds to stop working, we'd know by now.
The way I understand the story is that you have a scan of the relevant physical structure of the brain, plus the knowledge of how to simulate every component precisely enough. You may not know how different parts interact with each other, but that doesn't prevent correct functioning.
Just like you can have somebody assemble a complex device by just putting together pieces and following instructions. You could for instance assemble a working analog TV without understanding how it works. It's enough to have the required parts, and a wiring plan. Once you have a working device then you can poke at it and try and figure out what different parts of it do.
