Fsck never deletes possibly bad data; instead it will be moved to `.git/annex/bad/` for you to recover. Here is a sample of what fsck might say about a badly messed up annex: $ git annex fsck fsck my_cool_big_file (checksum...) git-annex: Bad file content; moved to .git/annex/bad/SHA1:7da006579dd64330eb2456001fd01948430572f2 git-annex: ** No known copies exist of my_cool_big_file failed fsck important_file git-annex: Only 1 of 2 copies exist. Run git annex get somewhere else to back it up. failed git-annex: 2 failed