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: NUMBER KEY 1 SHA256E-s15766010--8132a02a8b245eb9842e89c5e696df4e9c82d676f8dec3c6bb96892c19f99d51.jpg To remove unwanted data: git-annex dropunused NUMBER ok (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 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 [[bugs/done]].