Even collections with books only from Amazon are affected also. The new software decided that I can't sort by or display collections from prior to the software update.
ETA; I went to my Amazon account and deleted the old collections. Making new collections on Amazon does not allow them to display on the Kindle; that sucks.
I was able to transfer my own work and that of other authors who have given me their e-books to the Kindle from Calibre without problems.