Most likely an issue from using the infamous Auto Defect connectivity mode. The player comes set to this mode by default and can connect in either MTP or MSC mode without your knowledge. Files loaded in one mode cannot be seen by your computer (or you) while connected in the other, giving the illusion of missing files or hidden ‘used’ memory space.
If you really want to clear the player, freeing up all the memory and start over, you can use the Format command in the Setting > System Settings menu. Then choose one of the 2 USB modes (also in System Settings) and stick to that. MSC (Mass Storage Class) is generally preferred unless you use Rhapsody, Audible, Overdrive (library) or other DRM-encrypted files.
