Hi there,
If this post this in the wrong forum, feel free to direct me elsewhere.
I have this issue today. The situation is that I wanted to transfer a book from Calibre to my Nook Simple Touch as I have done so many times before. But something went wrong today. I got an error message about failing communication. Nothing was reported faulty until I tried to transfer the book, which is why I'm lead to believe that it's Calibre which does something.
Anyway, now Windows reports errors on my device when I connect it. It can not repair these errors. I tried all sorts of things. Copying the file manually doesn't work, since windows reports "no room available". It happens on both the internal memory and the sd-card. The sd-card is reported as faulty on Windows as well. Turning it off and on again *sigh* didn't do anything. Neither did a reboot. I can't format the device on Windows either, which is probably a good thing in most cases.
I tried a factory reset, but something goes wrong when connecting to B&N for the deactivation. And when the deactivation goes wrong, the reset will not complete.
And now the weird thing: I found a laptop I have which runs Ubuntu and installed Calibre on that. I formatted the Nook on Ubuntu (without issue) and restarted it, and now everything worked. I could transfer books, I could read the books. Huzzah! Or so I thought. Because as soon as I plug it back in to my Windows PC, the problems are exactly the same as before , and I still can't copy books to the Nook from Windows explorer either.
Just to make matters worse I thought at that point that it was my Nook which was to blame. So I tried my wife's Nook (same exact model), and now I messed that up as well.

Exactly the same symptoms too.
I'm running latest version of Calibre 3.3.0 on windows (disabling all plugins was tried, of course). The one I downloaded on Ubuntu which works is version 2.55. I wonder if that's the deciding factor?
Windows 10 Pro with all the latest updates, bells and whistles in terms of updates and patches.
...and of course a pair of now slightly paperweighty Nook Simple Touch
Any and all suggestions are very appreciated.
Thanks in advance.