So i tried experimenting with the game a bit to figure out what's wrong with the disappearance of the safe files and I found out that when playing the game for a couple of times for some time, (I replayed the game fore like 5 times from start till the end of the build in the beach cave) for some reason when I looked at the www folder and then the save folder, everything there seems to be empty. Is this some sort of bug when I finished playing the build?  

You need to save, there is no autosave. From the main menu or at a save statue and save your game to a save slot there.