When you're booted in cm7, and you plug your NC into your computer, how many disks do you see (that you can actually write to and read from?)
I would drop a file into each of those, at the top of it, and call it "cmdisk 1" "cmdisk2" etc. just so you know which partitions are visible to your computer, then copy files to a place you know you can see from your computer and copy them off, so you're sure you have them to put back into the stock OS.
I would be really interested in knowing the outcome of that experiment, and also whether, when you boot back into stock OS, either of those files are still visible to the Nook OS and to your computer.
My memory is that CM7 treats the internal storage as its "sd card" when you're booting from the card, but I don't know which partition it calls the "sd card" -- the partition that your computer can see (/media) or one of the others.
It sounds as if CM7 saved at least one and maybe both of these either to its own or to your Nook's /data partition by default.
The behavior is very interesting to me just now because there's an odd thing happening with how CM7 on the NT is seeing storage. Folks have been trying to reformat partitions on the SD card and wiping their boot partitions instead.
This past weekend, I spent a little time looking at the NC and NT files that control /media and /sdcard, and emerged confused about what level of control over that is possible. (vold.conf and vold.fstab; I wasn't busy bricking an NT, but I was trying to get an NT to behave a bit unusually.)
For the most part I run stock OS. Not long ago I need to get a library book without sideloading, so I switched over to my CM7 side and using Overdrive, downloaded a book. I thought it would save to the uSD, but when I connect to my PC, I don't see it. Did it save it on my NC in the hidden portion?
When you initially download a book using Overdrive, the only thing present on SD is an .acsm file in the /sdcard/overdrive folder. If you click on that in a file explorer, it will offer to open it in a suitable reader (e.g. Aldiko). You must have Aldiko registered as an Adobe device, but once you do that, you can import the file, and the actual DRM-encumbered epub will be downloaded.
My experience differs. I open the Overdrive app, go to the Menu, select search for books, select my public library, do the search, select my book, then hit the download button, and the book downloads, apparently to a partition I can't see. Then I open the Overdrive app again, and the book is there as one of my choices, I open and read.