Ok, I think your post is in the wrong place. Should be in Nook Apps, QA, but here goes anyway.
First, I'm going to assume that by "e-reader" you meant the old B&N eReader software, and not the software from eReader.com. Those two were different and incompatible (even tho B&N owns both companies).
There was some differences in the older versions of B&N eReader as to where they stored books. When I upgraded, I had to go dig around in my file system and drag things from one place to another. It had to do with what you told it was your library location when you installed.
But if your books were all B&N books anyway, it might be easier to just re-download them from your B&N account. (See settings to make sure it is all correct). Then Library, All Items, and download again.
Are you referring to the NOOK for PC App? If so, try this to make it reappear:Make sure that there is nothing in the search box (clear the search box) and clicking on the x next to the space
THEN clicking on All Items underneath My Library