If some files are hardlinks, %fdupes does not work properly, and it is not
capable to link duplicates.

mkdir a
mkdir b
echo >a/x
cp -a a/x b/z
ln a/x a/y

Now run
%fdupes b a

It will do:
���a/x��� => ���b/z���


Before:
a:
total 52
drwxr-xr-x   2 sb users  4096 Aug  2 17:51 .
drwxr-xr-x 277 sb users 36864 Aug  2 17:51 ..
-rw-r--r--   2 sb users     1 Aug  2 17:51 x
-rw-r--r--   2 sb users     1 Aug  2 17:51 y

b:
total 48
drwxr-xr-x   2 sb users  4096 Aug  2 17:51 .
drwxr-xr-x 277 sb users 36864 Aug  2 17:51 ..
-rw-r--r--   1 sb users     1 Aug  2 17:51 z


After:
a:
total 52
drwxr-xr-x   2 sb users  4096 Aug  2 17:52 .
drwxr-xr-x 277 sb users 36864 Aug  2 17:51 ..
-rw-r--r--   2 sb users     1 Aug  2 17:51 x
-rw-r--r--   1 sb users     1 Aug  2 17:51 y

b:
total 48
drwxr-xr-x   2 sb users  4096 Aug  2 17:51 .
drwxr-xr-x 277 sb users 36864 Aug  2 17:51 ..
-rw-r--r--   2 sb users     1 Aug  2 17:51 z


=> y is unlinked from x and linked with z. The result is missing hard link that
existed before.