Regardless of the length of the war, crushing Unionists and unruly slaves would be the first post-war task of the Confederate armies. I expect most will be given the same chance that the UCT Tennessee Unionists were given at Ft Pillow and be massacred, though some may fight their way to Union territory. There's also a good chance the Confederate government will force a Trail of Tears on white Unionist civilians.
Many Appalachians can be very stubborn and feel very tied to the land(also forcing whites out like natives are harder to justify and do most of the time). Many rather keep fighting or just hide deep in the mountains(a lot of places to hide). Flip floppers will also be common. These people often didn’t care about slavery that much morally. Some just hated southern elites and lower south for its own personal reasons so they joined the union. You had some people attack both the union and confederates at different points of the war(the war in this area was more local confederates vs local unionist then anything else). They just don’t like people “imposing” on them. That’s what makes situation there crazy. They honestly might be too busy killing each in Appalachia(like in the civil war and reconstruction). CSA did have a decent amount of support there(plural or slight majority depending on area). North Carolina Appalachia didn’t turn more union until the governor put in place his more intense draft laws. Appalachia is a issue for both nations because the locals often only care about their own grievances and either don’t care about outside world or are even hostile towards it. The union and confederates could be giving guns to partisans to fight each other but those partisans could easily end up attacking them too. Appalachia isn’t going to be pleasant on either side of the border and locals might start hating each side more and more. Some will even think about Appalachian independence given the strong regionalism(neither the confederates or union would want this. It would almost split the CSA in half and the union doesn’t want to lose more states especially on the CSA border. Both sides won’t tolerate an independent movement especially if it is socialist in some of its beliefs).
Let’s say you have some unionist in CSA Appalachia flee right across the border into West Virginia and Kentucky where the CSA can’t get them. Them doing cross border raids and attacks as an act of revenge even if done independently is likely because they can run back and forth across the border to safety pretty easily since they know the land well(that area where Virginia, Kentucky, and West Virginia is the heart of the Appalachian mountains that would be very hard to prevent small groups from crossing either way if someone wanted too). The union might see this and think “enemy of my enemies are friends” not realizing these people often don’t like them either but hate the confederates more(at the movement). So they give them union made guns and let them set up base on the border to cause trouble for the confederates(more passive in nature these groups are often acting on their own and the union support is more like “why not, let them cause trouble for confederates. We will even give yall some guns”. The confederate either use force or try to flip some by giving them back there land(very important to them but some are likely still to refuse).
The issue comes when coal barons, companies, and company towns become common in union Appalachia. Many of those people even the ones they armed will think those groups I mention(not the actual government yet but businesses in the area) are no better then the southerner elites if not worse. What would happen if partisan groups the union was funding to fight confederates decided to attack company towns(with local assistance) in West Virginia and Kentucky especially if these towns are own by New Englanders or northerners? Those companies are going to wonder “wait how did a bunch of hillbillies get well manufactured union guns” and if they find out its from the government they will be pissed and many within the north will be upset too. It’s also likely many of the local residents assist them if they attack these groups. They could also be funded by non government groups in the north who think they hate the confederates for the same reasons they do which can lead to similar issues when they turn against them. This would put the US government in a tough position. Funding partisans isn’t going to be taken well by some internationally(Europeans have stigma about this type of stuff. They often found it “unfitting of civilized people”), public up north going to be piss when they find out especially businesses, and the south will use this to point finger(trying to direct stuff towards the north to cover up their own stuff), and finally the north might lose local support in the area depending on how they handle this. The north is likely to support businesses over people like otl which means they are seen as part of them.
The US is still making this mistake and has done so in the past with partisans. They give weapons off of “enemy of my enemy is a friend” logic not looking more into it(Syria, Iraq, and Afghanistan are good examples. They often give weapons to coalition or partisan forces not realizing many might become something else later on or not taking into account them trading weapons to other groups they do not support. The US doesn’t intentionally create terrorist groups. They unintentionally do it because they often throw money and resources at their problems without taking everything into account). CSA doesn’t have as much money to throw so their methods will be more force or concessions(free land or materials as a form of bribery). The government of both nations actually might be the more rational ones in this while they have individual groups and people doing reckless stuff. The north will likely not go to war over border issues because they will see it as cheaper and easier to solve issue from within(a very hard problem to solve). People from New York City or Boston isn’t going to see “a bunch of hillbillies and rednecks acting like thugs and criminals in the border regions worth a costly war and re-integrating the south”. Many prefer a proxy type conflict over an actual war. Also you can’t always just start a war over acts of independent people and groups. The issue with this though it makes it where both governments can easily deny responsibility for a lot of things. When you have people on both sides of the border doing their own things actual government funded forces can cross the border and cause trouble because both can easily throw them under the bus if they get caught by claiming those people have “no ties to the government”. It’s like using Bid Laden as an excuse to invade Saudi or using cartel as an excuse to invade Mexico(kidnapping of citizens and guns are common on the US-Mexican border but we don’t invade the place). It might have some valid points but no one sees it worth the trouble or a realistic choice. The confederates will likely have officials in government doing their own thing too. The confederates probably labeled a lot of groups like this as illegal or criminals but like Mexico does a very poor job at stopping them because they have people in the government, military, and even some public support.
For example, Jesse James does his otl stuff. He attacks union businesses, rails, and government stuff in Missouri and Kansas. The union can’t catch him because he flees over to Arkansas and Oklahoma when in trouble. This is where he sets up base. The confederates government consider him a criminal but much of the public in the south romanticize him and see him as a “freedom fighter”. Some locals in the confederate states and even southern Missouri help him. People in law enforcement in the south often are sympathetic to him or even work with him at times and he even brides people on both sides a lot. The north is very annoyed with his actions especially towards the railroads. The south “officially” see him as a criminal so they can’t take action against him there especially with how unwilling the confederate government is to lose face to the US(they can’t send forces into the country like Mexico). The US can either catch him in Missouri or fund/bribe people to kill him in the CSA(CSA doesn’t lose face but has to be careful not to make it look like government did it because the public sees him as a Robin Hood character. CSA also has to worry about people tipping him off from within government). The border regions will have a lot of grey points and be very blurred in most issues. You have a lot of people in both countries acting on impulses and their own interests. A lot of the partisans will likely be making money in criminal ways too. Jesse James could steal bonds from the union and sell them somewhere in the south. Outlaws out west might kidnap blacks in the union and sell them in the south. Some American people are often going to be playing both governments to their advantage. If the CSA tried to force me out of the country for being a unionist I could easily go to a rural area re enter the country under a new name and identity in a different area of the CSA. Same goes for the other way around with the union.