I guess I lucked out that I only lost a few of my books from Fictionwise. I hadn't planned to even register at B&N, but then thought what the heck. I appreciated that they made many of the books I had purchased in LIT format available as ePub. It took some months before download links appeared on all of them and some have since gone away, so I'm glad I have those files backed up already.
The Borders to Kobo transfer didn't go very smoothly for me. Which was surprising since the Borders ebooks were "powered by Kobo"
But it took a long while before the Borders books showed up in my Kobo library and I lost a few there too.