This is a common mis-understanding of how files get added to your device. There are 2 USB connection modes, MTP & MSC. But there’s also a 3rd choice on your player in Settings > System Settings USB Mode . . . Auto Detect, or as we like to refer to it here, Auto De f ect.
In this mode, your player will connect in MTP mode whenever possible, but when it’s not it will fall back to MSC mode. It doesn’t ask you if you want it to, or tell you that it’s doing this, so by using the Auto setting you sometimes end up with some files transferred via both modes.
But here’s the rub . . . files added in 1 mode (let’s say MTP) cannot be seen or accessed on your computer while you are connected in the other mode (MSC). So you end up as you are now, unable to see & manage all of your files and extremely confused and/or frustrated.
The solution is to pick 1 mode and stick with it, and not to use the Auto Defect setting. Which mode is best? It depends on how you want to (or plan to) use your player. Do you subscribe, or plan to subscribe to Rhapsody music service, or ‘borrow’ digital audio books from your local library or rent them from Audible.com? Then you would need MTP mode as it is required for any DRM (Digital Rights Muck)-crippled files as I’ve listed here. Do you plan to ‘sync’ your music from your computer using Windows Media Player? Then you’re stuck with MTP and its ‘virtual’ mode.
If you rip your own CD’s or buy plain, unadulterated .mp3 files from Amazon, E-Music, or other on-line music “purchasing” site, then MSC mode is your new best friend. In this mode, you will see your player as 2 separate drives with their own drive letter designation (like F: and G: ). The 1st one is the player (internal memory) and the 2nd is the external memory card slot. This will happen whether there’s a card inserted or not. You can now simply drag & drop the files you want from your computer to either the player or the card (if you have one).
So, given your situation, I’d recommend formatting the player which will erase all the files as JK98 already mentioned. Then set your player to one of the manual USB modes and re-load all your content. A pain in the lower rear extremity? You bet. But once it’s done, it’s done; and you will be able to see and do whatever you want to your files just like they were on your computer. Formatting is easy; there’s an on-board function on your player also located in the Settings > System Settings menu. Re-loading is up to you. Yes, your same folder structure (Music, Podcasts, Audiobooks, etc.) will still be in place.
All in all, it’s not so bad. The hard part is understanding on these things work. And hopefully this will have explained it adequately for you. If you have any other questions, just post back. Enjoy your toy!