Theoretically, you could probably do it with a macro recorder (a tool that records your mouse and keyboard inputs and then plays it back repeatedly).
A simple recording of mouse clicks and keystrokes could do it, for example, if you copy all your FS files into one folder, then record yourself opening the first file in the folder, exporting it to an EPS in another folder, then deleting the first FS file in the original folder. That sequence on repeat would probably work, with the caveat that the length of time that each export takes could cause problems, unless you leave a long delay in that part of the recording.