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I have a question, namely I saved the games from here on another hard drive and if I delete the save file there they are still there. Where are they still stored?
Provided you are on windows and the games you're talking about are based on the RenPy engine take a look at the folders you find in C:\Users\Username\AppData\Roaming\RenPy\.
Many other engines / games also store their saves in one of AppData's subfolder. Gotta poke around a bit...