Same thing happened to me. I had automatic scheduled transfers for every day of the week, and an additional big monthly one. They're all gone from the "Scheduled Transfers" list now.
Also, under "Past Transfers", the most recently scheduled automatic transfers (including the big monthly one set to happen in early June) are shown as "Failed." Prosper must have cancelled them all.
So here is what I believe to be the scoop. Any standing orders you had before Prosper 2.0 will poof the first time they fail (they may poof the first time they execute, pass or fail). I have setup new standing orders since they have been back up and these are behaving the way they always have.
Actually, standing transfers I recreated *after* the event were also canceled. Prosper's response to me was rather curt, merely indicating that the issue was "fixed," without offering an apology or an explanation.
I have not been back yet, since I may have enough remaining orders to clear my account on a weekly basis.