$ git init ; git annex init test ; dd if=/dev/urandom of=file1 count=128 ; cp file1 file2 ; git annex add --backend=SHA1 file? ; git commit -m init ; git annex unannex ; ls -l
Initialized empty Git repository in /tmp/annex/.git/
init test ok
128+0 records in
128+0 records out
65536 bytes (66 kB) copied, 0.007173 s, 9.1 MB/s
add file1 (checksum...) ok
add file2 (checksum...) ok
(Recording state in git...)
[master (root-commit) 2177b10] init
 2 files changed, 2 insertions(+), 0 deletions(-)
 create mode 120000 file1
 create mode 120000 file2
unannex file1 ok
(Recording state in git...)
[master bef78b1] content removed from git annex
 1 files changed, 0 insertions(+), 1 deletions(-)
 delete mode 120000 file1
total 72
-rw-r--r-- 1 simons users 65536 Jul 15 17:29 file1
lrwxrwxrwx 1 simons users   132 Jul 15 17:29 file2 -> .git/annex/objects/jp/Fk/SHA1-s65536--795b58cc4e5190b02e7026fd9e94a10c98c6475f/SHA1-s65536--795b58cc4e5190b02e7026fd9e94a10c98c6475f

This was recently discussed in annex unannex/uninit should handle copies and unannex --fast added to leave contents behind in the annex, which allows handling copies. But needs manual cleanup later with dropunused. --Joey