I have this exact same problem. I tried creating an empty metadata file so it 
can write over it, but that didn't work.
I decided to symlink only the folder inside '.cache/deja-dup', the folder named 
6724d3f170e0390931977a130c2b7632. I thought by leaving the deja-dup folder, it 
will be able to write the metadata file but still have everything else symlink 
somewhere else. It didn't work, and it was nasty. As soon as I tried to ran a 
manual backup (from the GUI, of course) I saw this error:

"Specified archive directory '/home/[user]/.cache/deja-
dup/6724d3f170e0390931977a130c2b7632' does not exist, or is not a
directory"

Well, I guess it's technically not a directory, it's a symlink to one.

Has anybody come up with a workaround for this? Anything?

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https://bugs.launchpad.net/bugs/1217959

Title:
  'metadata' file not found when creating backup ("Could not restore
  ‘/home/user /.cache/deja-dup/metadata’: File not found in backup"

Status in Déjà Dup:
  Confirmed
Status in duplicity package in Ubuntu:
  Incomplete

Bug description:
  Linux release: Ubuntu 13.04 64bit
  Kernel: 3.8.0-29-generic
  Python: 2.7.4
  Deja Dup: 26.0
  Duplicity: 0.6.21

  Hi. I've tried to do my monthly or so backup recently, but Deja Dup
  crashed after trying to backup a very large file (VM disk with Windows
  7, 50GB or so). I tried to do another one, this time excluding all my
  large VM's. However, now when trying to do a backup I'm getting the
  following error a few seconds after inputting my encryption password:

  Could not restore ‘/home/tom/.cache/deja-dup/metadata’: File not found
  in backup

  I've tried reinstalling both deja-dup and duplicity, purging
  duplicity, deleting deja-dup and duplicity from /home/tom/.cache,
  deleting the backup files on the external drive, deleting it's config
  as described here http://askubuntu.com/questions/53980/how-to-delete-
  all-the-settings-for-deja-dup. I know (well, I have some evidence
  supporting this) that the drive itself isn't faulty as I managed to
  backup my old laptop to the drive using duplicity and it worked fine
  (Fedora 19, deja dup 26.0 I think). I will upload the appropriate logs
  momentarily.

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