Using cp -R to copy your hardlinked data is removing the hardlinks.
$ du -sh one/ two/
140M one
4.0K two
$ cd one
~/one$ ln file1 file2
~/one$ ls -s
total 285280
142640 file1 142640 file2
$ cd ..
$ du -sh one two
140M one
4.0K two
At this point ls shows two 140MB files, but they are hard linked, so du reports just 140MB in use.
$ cp -R ../one/* two/
$ du -sh one two
140M one
279M two
This shows that cp -R doesn't preserve the hardlink status.
The (or at least, one) right way to copy this is to use rsync again, with the -H (or --hard-links) parameter.
rsync -avPH one/ three
sending incremental file list
./
file2
146058808 100% 185.43MB/s 0:00:00 (xfer#1, to-check=0/3)
file1 => file2
sent 146076781 bytes received 47 bytes 292153656.00 bytes/sec
total size is 292117616 speedup is 2.00
$ ls -s three/
total 285272
142636 file1 142636 file2
$ du -sh three
140M three