Truth be told, I tried a lot of things - deleting the persistent file does not work, you need to actually replace it with an older version of the file. Which can be kind of a headache, but life. I still think this should not be a trend. You either let people choose if they want this kind of thing active on their playthrough or not. Otherwise it kind of defeats the purpose of a save file.
Luckily, I tend to mess around with the save files a bit at times, so I made a duplicate of the folder at one point. Won't be able to skip some of the "seen text" but at least I managed to fix this. I also found how to re-enable scroll back feature, which is kind of cool, will help me if I ever get back to some older games I haven't touched in a while.