Ok so my issue was that my save folder was on my documents path
I have re-installed the game, this time my save folder was located on my user path, I have then re-enabled my cloud save then an error appeared, asking me to choose between the cloud or local save, I chose the local save then it works.
For anyone wondering why its not working only remove the "Slot0" file, then add the modded "Slot0" and then turn of steam cloud for beyond two souls by Right-click on the game in the Steam Library, select Properties, and then toggle the Cloud Synchronization setting under the General tab, dont know why no one has complained about this in the comments but yeah
Start the game, while the game is running rewrite save file and close the game. Steam cloud will take my save file and upload it. After that you should be able to play my save file and get achievement. Obviously, back up your own save file, just in case.
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I have re-installed the game, this time my save folder was located on my user path, I have then re-enabled my cloud save then an error appeared, asking me to choose between the cloud or local save, I chose the local save then it works.