Note that the rsync '-a' (archive mode) does not preserve hard links:

$ ls -li inc*
107256 -rw------- 3 tong tong 10 03-23 10:33 inc.txt
107544 lrwxrwxrwx 1 tong tong  7 03-23 12:13 inc2.txt -> inc.txt
107256 -rw------- 3 tong tong 10 03-23 10:33 inc31.txt
107256 -rw------- 3 tong tong 10 03-23 10:33 inc32.txt

rsync -vua . /tmp/lnk_tst
cd /tmp/lnk_tst

$ ls -li inc*
217084 -rw------- 1 tong tong 10 03-23 10:33 inc.txt
217061 lrwxrwxrwx 1 tong tong  7 06-02 11:47 inc2.txt -> inc.txt
217085 -rw------- 1 tong tong 10 03-23 10:33 inc31.txt
217086 -rw------- 1 tong tong 10 03-23 10:33 inc32.txt

For the rsync command to preserve hard links, use an extra -H:

-H, --hard-links            preserve hard links

rm -rf /tmp/lnk_tst
rsync -vuaH . /tmp/lnk_tst
cd /tmp/lnk_tst

$ ls -li inc*
217067 -rw------- 3 tong tong 10 03-23 10:33 inc.txt
216974 lrwxrwxrwx 1 tong tong  7 06-28 16:44 inc2.txt -> inc.txt
217067 -rw------- 3 tong tong 10 03-23 10:33 inc31.txt
217067 -rw------- 3 tong tong 10 03-23 10:33 inc32.txt

$ rsync -v
rsync  version 2.6.9  protocol version 29

To copy files while preserving hard links, use tar:

mkdir /tmp/lnk_tst2
tar -cSf - . | tar -xvSpf - -C /tmp/lnk_tst2
cd /tmp/lnk_tst2

$ ls -li inc*
217117 -rw------- 3 tong tong 10 03-23 10:33 inc.txt
217118 lrwxrwxrwx 1 tong tong  7 06-02 11:55 inc2.txt -> inc.txt
217117 -rw------- 3 tong tong 10 03-23 10:33 inc31.txt
217117 -rw------- 3 tong tong 10 03-23 10:33 inc32.txt

$ tar --version
tar (GNU tar) 1.16

Well, actually 'cp -a' preserves hard links as well:

cp -a . /tmp/lnk_tst

$ ls -li /tmp/lnk_tst/inc*
217074 -rw------- 3 tong tong 10 03-23 10:33 /tmp/lnk_tst/inc.txt
217075 lrwxrwxrwx 1 tong tong  7 06-14 15:37 /tmp/lnk_tst/inc2.txt -> inc.txt
217074 -rw------- 3 tong tong 10 03-23 10:33 /tmp/lnk_tst/inc31.txt
217074 -rw------- 3 tong tong 10 03-23 10:33 /tmp/lnk_tst/inc32.txt

documented on: 2008-06-02