No, it would not be possible to edit it so that it thinks those characters are dead while they are part of your faction. This is why recruiting such characters is not allowed in vanilla, it can and will break certain systems.

Best you could do is one of two things.

1. Make a mod and delete the character, then load your save. When you load your save it will be unable to detect the character data for them, and will replace it with a default set of data instead. This will not affect their appearance or stats. Just background stuff like certain flags on the characters, world states, and dialog packages (which dialog packages won't matter here anyway since these characters don't have player dialog packages, as they're not intended to be playable). Afterward, you could disable the mod you made, import your save, then go kill the original NPC character to wipe out the group.

2. Make a mod to change the conditions of the world state. Find the world states that check the status of that character, and reverse them. If it checks that the character is not status 1, make it so that it's checking that they ARE status 1, etc. This will invert any world states involving them, meaning it will kill their faction as long as the character is alright, instead of killing the faction if they are dead.

I'm going to make a new mod. Seams the easiest way to do it

How do I delete them exactly?

Wait think I found it under characters testing it rn

So it worked for Dimak but not Tora. Plus now when I walk through the streets of Shek owned areas all the guards freak out and explain "It's Tora!" like when I turned in her bounty. They're not agroed it's just weird

Unless the Band of Bones are supposed to stick around in the fort between the desert and the hivers

turns out it didn't work for either Dimak or Tora. I used the Reactive World state checkers and even after "deleting" them they are considered alive

Did you do the part about removing the mod, then killing the bosses again?

Just deleting them will not flag them as dead. Deleting them forces your save to no longer associate your player characters with the unique character data. Afterward you would still have to remove the mod, then kill the NPC versions again.

I did try. This is how it went.

-Made mod deleting Tora and Dimak
-Activated mod and booted up my save
-Got error involving Dimak and Tora and game used fallbacks
-Went to Tower of Ninjas and it was already destroyed and had no faction assigned to it
-Went to camp of Exiles, could not find Tora
-Went North to the Man Hunter base that begins with an A (I forget the name).
-Base was filled with Band of Bones after I killed the Man Hunters so I thought Tora might be there
-Can't find Tora
-I use the Reactive World state checker to see if Tora and Dimak are still alive and it says they are

Also every time I go anywhere with Tora that's Shek controlled they act like I'm turning in her bounty again even if I'm not carrying her. Dounty Hunters say the same stuff about Dimak. I even trying importing while the mod was still active and the dialog still pops up.

You need to deactivate the mod. The steps should be

-Make mod deleting characters
-Activate mod and boot up save
-Get error about the missing character templates and it using fallbacks
-Save and exit game
-Deactivate mod
-Import save

Now after import, the original characters will be back again. Kill/capture them to trigger their world states.

I will try again however I no longer get the errors reguardless of the mod being on or off

Yeah, if you've ever saved with the mod on, the characters will not trigger the error anymore. That's fine, it just means that step is already done. :)

Do you know where Dimak will be if the Tower of Ninjas is already destoyed? Also no sign of Tora at Exile Camp, or ashigakira. I know she isn't at Greyflayer Village b/c it's still occupied by the Greylayers. You think I should just not import dead characters and start from scratch on my Shek war campaign?

I tried importing without dead people and Tora didn't even respawn. I think the game knows I have Dimak and Tora despite deleting them with the mod.

Same goes for Dimak. The game def somehow knows they are still around despite me following the steps exactly. This sounds dumb but maybe I "deleted" them incorrectly? I made a new mod, went to characters, right clicked on them, and then selected delete which then greyed out their names. I saved, exited the editor, and then went back into the editor to check the mod and the names were still greyed out which made me think I was successful. Am I missing a step?