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Are you doing it as a part of an Action? If so, the files are temporary files until they are closed by the Action, so they don't have a "normal" file path at the moment you're running your script. If that's the case you will have to do it in two parts, I'm afraid.
First run an Action to convert the files to PDFs, and then another one to process those PDF files and save them in the desired location.
Alternatively, you can try editing the settings of the first Action and change the output folder to the one where you want the files to end up, and that might work on its own...