If those books are B&N shop items, downloaded by the Nook, you won't see them on the file system via USB (unlike the first edition where the books can be moved from the device).
Why do you want them to appear to your computer?
If you want access to them on your computer, download the PC/Mac app (as the case may be), register it to your account, and then download the files to your PC as you wish.
This is a problem we're running into with our HD and HD+s too - files downloaded to custom folders (you add yourself) stop showing up sometimes.
The following worked -
1) Restarting PC and Nook.
2) Plugging in and plugging out without restarting.
My recommendation would be that if this doesn't work then just create a new folder everytime you have to add new books. And that if you have an SD Card then remove it for a while and see if that fixes the issue.
I know of one other solution. Unfortunately it's not straightforward.
1st) Download the Android SDK - http://developer.android.com/sdk/index.html
2nd) Go to the 'tools' folder. It'll usually be something like
F:\Program Files (x86)\Android\android-sdk\tools
3rd) Run ddms. Please plug in Nook before this step.
4th) In DDMS, tap on the barnesandnoble-nbnrv named item. Then Device on top right and File Explorer in Device Menu.
5th) Go to /mnt/media and /mnt/sdcard and see which of these has the folder in which you had books.
Figure out what directory there is.
6th) Open command prompt and go to your Android > platform tools directory. Something like: F:\Program Files (x86)\Android\android-sdk\platform-tools\
Type in 'adb' there to see list of commands (or read article at link below).
7th) Use adb to transfer files - http://android-dls.com/wiki/index.php?title=ADB
Okay, the folder "My Files" contains the following folders "Books", "Documents", Magazines", "Music", "Newspapers", "Nook Kids Recordings", "Pictures", and "Videos". Books, Pictures and Videos all have files in them. All these folders are being listed on the Nook when I uncollapse the folder "My Files". The pictures show up in the "Gallery" and the Video show up under movies in the "Library" along with my book titles. No files are on a "scan disk". When I hook up my Nook to my PC (Dell), go to "Computer" and see the BTNV400 and folders, I see "MY Files", but only "Documents and "Newspapers" at first. I have tried rebooting my computer and turned on and off the Nook. When I did a soft boot on the Nook and then plugged it in to the PC, I got "Magazines" added to the list. When I contacted B&N tech support, he recommended I add my files to the "Documents" folder. I did test that and yes, my files show up. The issue is will I have to do this for every type file I want to side load. Will the "Gallery" recognize JPEG files? Will my videos run?
Maybe I'll just take the damn thing back!~
Any way I can do a "restore to factory specs"?
Maybe I'll try your "Android download suggestion first....