Experience and skills aren't meant to persist across runs, so that's intended behavior (the same way it works in the story, Liz will have to earn her skills in each timeline).
I'm much more concerned about the save file issue. Are you running this locally or on a VM? Any user account weirdness that'd interfere with saving files to AppData? You can check C:/Users/(your name)/AppData/LocalLow/Anunnaki Games/New Pred in Town/NaninovelData/Saves to see if files are being recorded at all.
I'm now going to go on a little tangent. Because based on what you said about the skills are supposed to reset completely and you have to start from scratch every time, then the endless mode is pointless. The whole point of an endless mode is to see how far you can get and try to get further the next time with what you've earned. But as it stands now, it's almost impossible to make it through just the first wave without ending and refreshing to get the most favorable round possible. And that'll just end as soon as you get hit with a predator that is spamming more cards than you can right at the beginning and you can never get through its defense. At this point, you might as well not even put the skilled Tree in there if you're not going to let us keep the points that we put into it at all. And if you don't keep the skills that you unlock during the story mode whenever you start up another game then some scenarios will never be able to be beaten. For example when you get eaten going to the bathroom at that one point in the story. It is practically impossible to survive that without having skill points from a previous run in play, because they play anywhere from 2 to 5 cards while you can only play 2 or 3.
You're conflating two very different types of progression here. Have you played many roguelikes before? Generally, the kind of unlockables which persist between runs are intended to increase the number of options a player has rather than raw power.
In terms of general difficulty outside of Endless Mode - it's useful to know that players are having difficulty with Noriko. She's pretty easy to beat in my testing once you understand the mechanics, but given that she's the first available prey scene and you're far from the only person having trouble here, I'll think about how that scene might be toned down a bit.
I just tried the new update on the endless mode and it's not possible to beat the first boss. You would need so many points in both the prey and the Predator side just to win that fight that is not possible with the way it's currently set up. I may check out the game again later when more of the story is uploaded. But as for the endless mode, there has to be some sort of semblance of being able to beat the very first wave at least, otherwise, there's no point in playing it. I still have the original upload that allowed you to keep your skill points until you at least turn off the game. So that's the one I'm going to be playing when I want to play the endless mode. Because that's the only way it's actually fun and fair. Well, you can continue if you fail as the predator to digest your prey in endless mode, the run Ends when you fail as the prey, and there is a 95% chance that you're going to fail, because I've only ever survived it two times as pray out of the 30+ some runs I've played. There is realistically no way to progress past the first wave in Endless mode without the skills and cards carrying over, and yes I have played rogue-like games but they were balanced to be fair, this isn't.
