You have to look in the settings of 3M ChartScript Transcription to see exactly where the files are stored because I've downloaded all the PDF files and couldn't find anything related to file storage.
Start the software then go to the main menu until you find the settings. Additionally, access the built-in Help/user guide to look for these details.
I couldn't test the application since there is no download available and requires a master server where it connects to.