Comment 9 for bug 534651

I've figured out how to remove my 'orphaned' emblems with the following command:

gvfs-set-attribute <file> metadata::emblems ""

On the face of it, this command would appear to overwrite any existing emblem metadata with a single blank emblem, as the new output of the aforementioned output is:

attributes:
  metadata::emblems:

rather than:

attributes:

which appears to be the output of any icon with no assigned emblem metadata. In any case this has also solved my issue vis erroneous (?) emblems in docky; they are gone.