Is there any way to remove a permanent bounty in Skyrim?

I have basically made my Skyrim save unplayable, I had downloaded the Civil War Overhaul and done the first set up quests up until the defence of Whiterun. I did some thing that broke the quest chain and finally installed the mod and carried on with the standard civil war until I realized I was being instantly attacked in every Stormcloak city. I've attempted to yield, pay the bounty in console, set my overall bounty to 0 but absolutely nothing works. Does anybody have any idea on how to fix this problem with a mod/command?
Best Answer
There are two important points you missed, both contained within Civil War Overhaul description. Since mods creator, Apollo Down, is a masterfull wordsmith let me just quote the relevant bits from the Nexus page.
One - installing CWO during the gameplay:
YOU MUST START A NEW GAME. THERE IS NO WAY AROUND THIS. AT ALL. SO DON'T ASK ME. BECAUSE YOU MUST START A NEW GAME. YOU MUST START A NEW GAME. NO, NOT AFTER YOU EXIT HELGEN THE FIRST TIME, NOT BEFORE YOU START THE CIVIL WAR, NOT AFTER BREAKFAST,YOU MUST USE THIS ON A NEW GAME WHERE YOU CLICK ON THE TEXT IN THE MAIN MENU THAT SAYS 'NEW GAME'. YOU MUST START A NEW GAME.
Without following a requirement that clear you can't really expect help with any problems you encounter.
That said, point two - Stormcloaks attacking you.
Basically, after the first siege of Whiterun, the guards in holds your faction does not own will be hostile toward you. All enemy soldiers will be hostile to you as well. Let me say this again because I get a lot of questions about this: HALF OF SKYRIM WILL BE HOSTILE TO YOU. THIS INCLUDES CITY GUARDS IN HOLDS YOU DO NOT OWN. THE ONLY WAY TO STOP THEM FROM BEING HOSTILE IS TO DISGUISE YOURSELF IN THE OTHER SIDE'S ARMOR, OR TO TAKE THE HOLD FOR YOURSELF.
What you see is not a bug. It's a feature introduced by the mod you just installed. One of the first features it advertises. So either you wear a disguise or uninstall that mod and hope that this script does not stay active.
Also, reading mods descriptions will go a long way for a healthy Skyrim modding experience.
Pictures about "Is there any way to remove a permanent bounty in Skyrim?"



Is there a way to get rid of bounty without paying Skyrim?
There are three main ways to get rid of a bounty: paying it, serving jail time, and using your Thaneship to get out of it. You can also try killing any witnesses or, if you're a Thieves Guild member, bribing your way out.How do I get rid of a 1000 bounty in Skyrim?
Bribe guard Thieves Guild members have the option to bribe the guard. The amount of gold required to bribe a guard is usually much larger than the bounty for small crimes, but less than one for murder and doing so will raise the Speech skill, immediately clear your bounty and avoid having items confiscated.How long until bounty goes away in Skyrim?
Avoid the town and just continue playing in the rest of the world. An NPC bounty hunter will come after you and he'll actually talk first, giving you the option to pay the bounty and it'll clear it up. Show activity on this post. Leave town and wait 48 hours if all the people are attacking you in the town.Who can clear my bounty in Skyrim?
Bribe guard Thieves Guild members have the option to bribe the guard. The amount of gold required to bribe a guard is usually much larger than the bounty for small crimes, but less than one for murder and doing so will raise the Speech skill, immediately clear your bounty and avoid having items confiscated.Skyrim How to clear your bounty and NOT lose your stolen goods.
Sources: Stack Exchange - This article follows the attribution requirements of Stack Exchange and is licensed under CC BY-SA 3.0.
Images: Nataliya Vaitkevich, Pixabay, veeterzy, Joshua Welch