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