You may have set up the system to save everything in two different places. This is not typical, but for example, if you set up the default config location (where you setup your default directory locations for: Data, Methods and Sequences) for one drive path and your individual method and files to over-ride it and save everything to another location, then you might end up with two copies.
BTW: I do not understand your comments about right side and left side data. ChemStation works with METHODS, that you create (please do not overwrite them!) for a specific task or application. Within the method is a Run Time Checklist, you select if data analysis is part of the method, and if so, if you also want to automate reports too. Within the method, you will have one or more detector set-up screens. Within those screens you can select signals, choose their properties and optionally "Save" them as part of the method. In the Report section, you can select output types. This includes files and/or reports. ALL of these things are part of one method and when you save the method, you save all the choices you made (you can of course go back and edit them later). So there are lots of places where you could request that the system save specific files as part of the method and store them (somewhere). Use the "Edit entire Method" feature to step you through all of the logical screens so you can review them. If you have not done so already, I would strongly recommend taking a training class in the use of ChemStation too. It is super easy to use, very logically laid out and organized. However, if you have used some other system before, it may appear odd at first (change always make people dislike the "new" system at first).