This is an old thread, however I just experienced the same problem as @hopkinsje, and happened to also resolve the problem.
PROBLEM:
Alfred workflows and all preferences went missing.
WHAT CAUSED THE PROBLEM:
I was running out of space on my Mac's hard drive, so I started to update Dropbox's Selective Settings, turing off large folders that were eating my HD space. I accidentally turned off the Dropbox folder that I was using to sync my Alfred settings.
SOLUTION:
Re-enable Dropbox syncing for my Alfred folder.