Where did the list of flagged message go in Mavericks Mail?
I had this problem -- the "Flagged" folder disappeared from the Mail app and no longer contained any flagged messages, even though I could see that my messages still had flags if I logged into the iCloud website and looked at them there.

For me, the solution was to rebuild my Inbox in the Mail app.  Select the mailbox you want to rebuild ("Inbox" in this case), go to the Mailbox menu, and select "Rebuild" at the bottom of the menu.  It could take a minute or two, depending on how many messages you have.  Suddenly Mail recognized all the flags again, and my Flagged folder re-appeared with my flagged messages in it.