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My first time through the game was a fantastic experience when it originally released on Gog. A couple days ago I decided to try playing it again and it's completely busted. Several areas I haven't been to yet are already have random control points unlocked, scripted quest bits aren't firing, it just isn't playable. It's like certain pieces of my original playthrough are persisting regardless of game status.

I did some digging and apparently this is a known issue they never bothered to fix.

I'm basically going to have to purge every bit of save data from existence in order for the game to be playable. This is not ok, and completely defeats the purpose of having the option for chapter selection.
I just beat the game, and started a new playthrough, and I'm fine so far. An hour in, just got past the janitor's office and seems fine so far. I'm not sure, sorry :(
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Heartstopper: My first time through the game was a fantastic experience when it originally released on Gog. A couple days ago I decided to try playing it again and it's completely busted. Several areas I haven't been to yet are already have random control points unlocked, scripted quest bits aren't firing, it just isn't playable. It's like certain pieces of my original playthrough are persisting regardless of game status.

I did some digging and apparently this is a known issue they never bothered to fix.

I'm basically going to have to purge every bit of save data from existence in order for the game to be playable. This is not ok, and completely defeats the purpose of having the option for chapter selection.
I have the same issue. After starting a new game it seems some things are not reset making the game almost unplayable. My solution: turn off cloud sync for Control, Backup and delete your save game in C:\user\you\documents\my games\control . Now start a new game. You can turn on cloud sync again now. Now you have the real fresh experience you should have.
yeah okay you're right, I'm stuck in in the furnace quest and this's 100% incompletable. Half the puzzle's done, and all the doors are stuck, and all the chests are open despite me never being here. damnit.
I thought I was going crazy, but apparently not. Subsequent playthroughs definitely feel like they're broken, with a lot of already opened crates, saved control points, buttons that won't give you the option to press them, and events that won't start like they should. I was able to find workarounds for a lot of them, but it is really clunky, which is a shame. It would be nice if they'd fix it, but given that the game is as old as it is, I doubt they will.

I'll give the workaround ferdinand suggested a try and see how it goes, but it would be a lot nicer if starting a new game meant starting a whole new game.
I was having a bit of trouble with "Control: Ultimate Edition" and came back to find this solution. It's worth noting I found my saved game files in my Admin account under "Users" after logging into the Admin account on my computer (I have several user accounts on my computer for Windows).