Overwrite Written History
You are on the right track when it comes to overriding history. The first step is obviously to remove the concrete evidence of the real history. However, simply removing the history would seem a little bit suspicious. Instead, you have to have some scholarly types come out and say, "after further research, we found that event x happened y way, and will continue with this going forward." This means that those still in school would begin to learn the new history and not the old history. Bonus points if you have some anti-family education going on, where the students learn to trust the teacher more than the government.
Remove physical evidence from the old history, on the basis that the old rulers lied to you, and your history is obviously more accurate. Show only artifacts to tell the story of the old regime horribly mistreating the populace and hopefully the members of the new regime. Establish a holiday to remember the horrible atrocities, and to mourn those lost in that event.
Shut out opposition
As you pointed out, simply replacing the concrete history doesn't eliminate the people that actually experienced it. However, most people probably didn't experience the history. Most people in your time period didn't travel very far, and thus have no real knowledge of the other holdouts. You can probably get away with saying that they gave up and fled, or were completely destroyed, since almost nobody is actually going to check. If someone does want to go check, then simply kill them en route and claim that they died from some other cause on the journey, or that some remnants from the old regime killed them for their new fealty, making them a martyr and increasing the peoples obedience towards the new regime.
If someone is able to evade your guards and wants to go check on the holdouts, they'll come back, and you can completely slander them. Shut them down for giving out "alternative facts" or simply trying to "spread rumors against the state." Remember, you have those poor poor martyrs that were killed by remnants of the old regime, and obviously any regime that still had a holdout wouldn't resort to such evil tactics, meaning that what the witness says is all a lie. Once the people are thoroughly convinced that they're lying, you can kill them under the guise of suicide or a heart attack and say "they weren't in the best of health" or "they were sad from being ostracized."
Control the modern narrative
The final stage is to control their live access to information. This may be harder than the modern day, but the premise still applies. Remember, you control what kind of notices can go out in the town square, so that is covered by simply delivering your regime's propaganda. Your real threat is going to be travelling merchants come the long way around from the holdouts, or interact with merchants that go there.
Obviously people would know something is up if merchants stopped coming altogether, however if there were merchants rumors about the road being blocked to the holdouts, or if a lot of merchants were killed by wolves or thieves along the way (preferably with a few limping their way back bloodied, giving out dying words about the thieves and wolves), then merchants would stop travelling there. They would assume that the holdout was abandoned, since now thieves (your goons) are able to act with impunity, and wolves are courageous enough to go there (a karambit or similar looks like claw marks, or you can just release wolves), and thus the logical conclusion is that they were conquered. This simultaneously makes life hell for the people actually living in the holdout, since they are left with only what they grow and what preserves they have. This also fits nicely with the idea that there was already little to no movement from these holdouts, as simply decreasing three or four down to zero isn't suspicious.
Left with no news of the holdouts, or limited news, the logical conclusion is that they all died fighting, holding on to their last bit of pride and honor. You can have a national holiday commemorating them for their valor in their last moments, and tell people that that level of patriotism is what we should all strive for in life.
Read alternative history conspiracy theories
Not for the alternative history (because it's mostly BS), but instead for the theories about how some lizard people supplanted the "real" history in favor of something that suits their narrative. My English teacher told me one time that "fiction has to make sense." If somebody pitched a movie detailing the 9/11 attacks back in 1990, it wouldn't get made because it would be too hard to suspend disbelief. Reality doesn't need to make sense, and that's why they were able to hijack a plane using some boxcutters. There already exists plenty of stories about replacing history, it's just a matter of sifting through that for the portions you want to include.
There's also plenty of variations on this theme in published fiction (although there is a higher pay wall there). I remember Terry Goodkinds Sword of Truth #5 had a narrative where an empire (your copy+paste Rome allegory )conquered a foreign land, integrated the inhabitants into their society, and the conquered people rose up in academia and politics to teach their own version of history and subjugate and shame the original natives, complete with mandatory daily "education."