I'm sorry to hear this, I'm really know very little about this area, but my understanding is that they will numb up the area with local anaethsetic first then make a small incision which a biopsy needle (thicker than a needle that would give an injection), there may be some sensation of this occuring, it shouldn't be pain, but some of the feelings can be so strong and unfamiliar that it feels like pain, this is where having some medicine to relax you first can be helpful - if it's not offered, but she feels she needs it she should ask for it.
I'm surprised by the necessity of going through the lung, the liver is an organ that can be accessed from many directions and you did say multiple things were there, so it would make sense to go for the easiest one to access, even then you have to be very still so the lung and the gall bladder aren't nicked in the process. If it really does involve going through the lung then she should be informed of the risks of doing this (pneumothorax, possibly leading to collapsed lung) and if she's not comfortable with them, to ask for a 2nd opinion - there are multiple ways of doing a liver biopsy.
The other thing to note is that as they've been doing stuff around that area, you can get some free blood inside and if this gets to the diaphragm, it irritates it and the pain from this can be very severe, but it's where you least expect it, as it's in the shoulder!
Just checking, but has she stopped any medicines that have a blood thinning effect, like asprin and NSAIDS (e.g. motrin, aleve, advil) and then some prescription ones.
My best guess is that she needs to be awake so the doctor can avoid the lung, rather then go through the lung in a particular state.
Cheers Anne