I used the save function in one of the passages and now the game starts from that particular passage and not from the beginning. Its obviously reading the saved file and loading the passage from it. Is there any method to reset it? (Deleting the save file will work, but I couldn't find the save location)
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To answer where the saves are located. There is no save file. Harlowe's saves are stored within the browser's Web Storage database, specifically localStorage. The easiest thing would probably be to use the Web Storage API via the browser's developer console to remove the save.
The story format itself does not do that automatically—which was my original point—it's something that the developer—I've been assuming that was you—thas to choose to place in their code.