According to the filing, MS and B&N have agreed to retire the existing Nook app for Windows 8. It's going to be replaced by a new reading app from Microsoft. This app has not yet been launched, but at the moment it is being called the Microsoft Consumer Reader. The new app will be co-branded with mentions of both Microsoft and Barnes & Noble.
Technically the filing says that B&N "would be permitted to discontinue distributing the NOOK Windows app". It makes the same statement about the Nook Windows Phone app, which has not yet been released (and now probably won't be).
While that does not explicitly say that the Nook app for Windows 8 is dead, I don't think I am misinterpreting the filing.
There aren't any details available yet as to what Microsoft's new reading app will do, but we did have some clue that it was coming. Microsoft has been dropping hints since late last year that they were interested in developing reading apps. In addition to the leaked details on a reading app for MS Office, there were also signs that Microsoft wanted to release a second app - more specifically, a consumer reading app.
I think I may have been the first to notice their interest; last October I pointed out that the R in the name for the Xbox MVR team stood for reading. My speculation was subsequently confirmed by a job listing which Microsoft posted in February 2014.
Update: A couple screenshots were included with the filing (found via Publisher's Lunch). As you can see in the images below, the new Microsoft app looks nothing like the existing Nook Windows 8 app.
Barnes & Noble has also been telegraphing that they no were longer interested in developing apps for Windows (or OSX); the Nook app for Windows 7/XP as well as the Nook app for OSX were formally abandoned last June after being neglected and ignored for well over a year. While B&N had continued to develop the Windows 8 app, it was pretty clear that they were under contractual obligation to do so.
Microsoft has been an investor in Nook Media since it was spun off of Barnes & Noble in early 2012. They initially invested $300 million in the firm, and they committed to paying up to another $300 million in operational costs (the exact amount has not been made public). The additional funds were dependent on B&N meeting certain goals in expanding the international Nook Store; as of the latest quarterly report B&N has not met the goals.