Bethany & Carver Missing

What mods do you have active and have you used the developer console?

I do have the developer's console enabled. I use it only for giving myself the mod items. I've never had any problems with my mods before - and I usually have the same ones installed every time I play DA2.

I have these mods installed: 

FOR NPCs:

• iveys Orana
• iveys Varania and Lia
• iveys Arianni and Nyssa
• iveys Tarohne and Idunna
• iveys Alistair and Teagan
• iveys Zevran
• Ishs Warden Nathaniel
• Grey Wardens in Dragon Age 2 (I downloaded all the mods in the pack - but deleted Warden Bethany and Warden Carver to see if that's what caused the glitch - it didn't)
• Dawn of the Seeker Cassandra

FOR Weapons & Armour:

• Branch of the Cursed Tree Barnstokkr II
• Anthracite Robe (both mage and rogue - but only have the mage one installed since I'm playing a mage)
• Amell Ancestral Arms
• Leap of Fate
• Dragon Knigth Armour Pack
• Eternal Vigilance Armour Pack
• Silverite-themed Champion Armour
• Orlesian Noble Light Armours
• Tallis Armor Retextures
• White Mage Champion Outfit
• Varric's Red Armour

FOR Chearts & God Items:

• MetaGame Abilities DA2

FOR Companions:

• The Fenris Files (Jacket in Black)
• DsC - DA2 - Fenris, Isabela, Anders, Sebastian (no Aveline because she's fine the way she is for me)
• Sebastian's Armour Retexture (Original Silver)

FOR Hair and Face:

• Chargen Revamp
• All Models
• Bidelles Cosmetics 2 (No eyes)
• Pineappletree's Vibrant Hair for DA2
• Pineappletree's Vibrant Colors for DA2
• Pineappletree's Vibrant Eyes for DA2
• Custome Female Hair Pack
• SG Beauty Shop
• LOTC's Hair Tints for DA2
• LOTC's DA2 Eyelash Fix
• LOTC's Skins for DA2
• LOTC's Female Eyelashes for DA2
• Natural Hair
• WyldTats and Skins
• KH Cosmetic Pack
• Lipsticks and Shadows
• Duchell's Textures - Skins and Scars
• More Hairstyles
• GoldSkins
• Polychromatic Soul
• Nathaniel Eye Fix

FOR Gameplay Effects and Changes:

• Better Mages
• Lock Bash
• Dragon Age II All Items Evolve
• Better Combat
• No More Bloody Teeth

FOR Models and Textures:

• DA2 NPC Hands

Taking at look at your list...

As a side note did you update to the latest patch when you reinstalled?

Yes, I installed it up to 1.04 - I also downloaded the High Resolution textures

"and missing overall in the fighting scenes. Like, they don't exist in the game. I hoped that once I was through the prologue they would reappear, but they didn't - and the cutscene where Varric shoots the pickpocket won't start at all. He just stands near one of the walls in Kirkwall doing nothing..."

It's not just cosmetic then (or not just cosmetic). Were the siblings present at all during the intro?

Here's what I'm thinking...

Either through a mod or console something has happened to Hawk's class, which has caused both siblings to die during the intro.

They haven't been present at all - invisible in all cutscenes but still talking - plus the non-existent icons on the lower left while walking around - it's like I'm soloing the prologue.

Yeah, but what?

I don't know if this will help but I found reference to invisible siblings in this post by heiro001 over on Nexus "Open the console again and type "runscript removetalent 300000". You need to do this to avoid the invisible sibling glitch." The thread itself is about switching siblings (Bethany over Carver).

You'll probably need to go back to the intro, so that quest will trigger properly once you arrive in Kirkwall and you might need to temporarily deactivate mods that change your skills until after the sibling dies.

** FYI According to the comments on Nexus Chargen Revamp hasn't been updated for 1.04.

So I am currently playing with mods etc... I had the same issue with carver after adding the mage class to my own hero as a warrior origin. doing this will automatically set the plot flag to mage origin, but you can play as a warrior with carver this way. 

I had an idea since carver was invisible but would join the conversations I had in gamlens house. If you've noticed, whenever a follower is in your party and you visit their home or active rest area where you can have conversations with them. they follow you around.

A simple way to fix this issue with your current origins sibling whichever was given as set by the plot flags, a simple command from the developer console will help solve this issue.

The Command is Runscript zz_(siblings name)_ debug and choose set at base. This will allow you to converse with your sibling within gamlen's house.