If you have a Pubit account, sing Glory Hallelujah! My advice is to have nothing to do with Nook Press, except for this Help Board. And don't change that policy until the users tell you that the storm is over; ignore B&N's "everything is peachy" PR announcements.
If you have new books to upload, upload them through Pubit. If you have the correct versions of EPUBs that Nook Press has corrupted, submit them through Pubit. If you want sales numbers, get them through Pubit.
Pubit still works. Nook Press's software is a sick joke. But every two weeks or so, they breathlessly inform us that they've added a new feature!
Ever wondered what would happen if a buggy-whip manufacturer set up an automobile-manufacturing division? Now you know.
In Pubit, if you go to My Titles > [particular book] > Actions > Edit > Upload Your Ebook > replace your ebook file--that's where you tell Pubit what EPUB file to upload. Click on "Replace & Preview," and preview your ebook on the virtual Nook. Then don't forget to go to the bottom of the screen and click on "I confirm that I have..." and "Save & Post Changes."
Your replacement EPUB will become the "official" EPUB that B&N downloads to purchasers, a very short time after you click "Save & Post Changes." Replacement time might even be instantaneous. This is the one way where B&N is better that Amazon; at Amazon, your changes have to be blessed by some guy in India before ebook-purchasers ever see them.