I assume you are referring to when you look at the files on your device using your PC's file explorer, not on the device itself? I find it a little inconvenient, until I remember that the individual files appear after the folders, when using the explorer in Win7. If you wish to change how files and folders are displayed on your PC, I guess you would have to see if there is an option for that, in your PC's file management software.
The SDR folders are not displayed when I use the File Browser in KOReader.
Luck;
Ken
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