Word summary: After migrating from SHA256 to SHA256E I still have a ton of SHA256 files around that aren't being found by unused.

Command outputs (see, specifically, the output of status showing number of SHA256 and SHA256E files):

greg@eeepc:/mnt/blackbox/Media/Pictures/Photos$ less .gitattributes
* annex.backend=SHA256E

greg@eeepc:/mnt/blackbox/Media/Pictures/Photos$ git-annex migrate .
(Recording state in git...)

greg@eeepc:/mnt/blackbox/Media/Pictures/Photos$ git-annex unused
unused . (checking for unused data...) (checking master...) (checking rose/master...) (checking x200s/master...)
  Some partially transferred data exists in temporary files:
    1       SHA256E-s15766010--8132a02a8b245eb9842e89c5e696df4e9c82d676f8dec3c6bb96892c19f99d51.jpg

  To remove unwanted data: git-annex dropunused NUMBER

(Recording state in git...)

greg@eeepc:/mnt/blackbox/Media/Pictures/Photos$ git-annex status
supported backends: SHA256E SHA1E SHA512E SHA224E SHA384E SHA256 SHA1 SHA512 SHA224 SHA384 WORM URL
supported remote types: git S3 bup directory rsync web hook
trusted repositories: 1
        c0e4106e-2631-11e2-9749-1bfa37a61069 -- rose
semitrusted repositories: 3
        00000000-0000-0000-0000-000000000001 -- web
        9bd4077e-196c-11e2-9cc9-9faafb3e34ee -- x200s
        c69d6fcc-18d1-11e2-9487-2fe6dbf0516b -- here (photos on eeepc)
untrusted repositories: 0
dead repositories: 1
        3ebd5ac2-2092-11e2-856a-bb0203cce179 -- Photos on Rose
transfers in progress: 
        downloading 2011/06/30/IMG_8180.jpg
 from rose
available local disk space: 2 terabytes (+1 megabyte reserved)
temporary directory size: 9 megabytes (clean up with git-annex unused)
local annex keys: 36210
local annex size: 136 gigabytes
known annex keys: 23388
known annex size: 102 gigabytes
bloom filter size: 16 mebibytes (7.2% full)
backend usage: 
        SHA256E: 37453
        SHA256: 22145
(Recording state in git...)

greg@eeepc:/mnt/blackbox/Media/Pictures/Photos$ apt-cache policy git-annex
  Installed: 3.20121017
  Candidate: 3.20121017
  Version table:
 *** 3.20121017 0
        600 http://ftp.us.debian.org/debian/ unstable/main i386 Packages
        100 /var/lib/dpkg/status
     3.20120629 0
        650 http://ftp.us.debian.org/debian/ wheezy/main i386 Packages

As Joey predicted, this took care of itself over time. Marking as done.