Note that -a does not preserve hardlinks, because
    finding multiply-linked files is expensive. You must separately specify -H. 
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-H, --hard-links
    This tells rsync to look for hard-linked files in the transfer and link together the corresponding files on the receiving side. Without this option, hard-linked files in the transfer are treated as though they were separate files. 
When you are updating a non-empty destination, this option only ensures
    that files that are hard-linked together on the source are hard-linked together on the destination. It does NOT currently endeavor to break already existing hard links on the destination that do not exist between the source files. Note, however, that if one or more extra-linked files have content changes, they will become unlinked when updated (assuming you are not using the --inplace option). 
Note that rsync can only detect hard links between files that are inside
    the transfer set. If rsync updates a file that has extra hard-link connections to files outside the transfer, that linkage will be broken. If you are tempted to use the --inplace option to avoid this breakage, be very careful that you know how your files are being updated so that you are certain that no unintended changes happen due to lingering hard links (and see the --inplace option for more caveats). 
If incremental recursion is active (see --recursive), rsync may transfer
    a missing hard-linked file before it finds that another link for that contents exists elsewhere in the hierarchy. This does not affect the accuracy of the transfer, just its efficiency. One way to avoid this is to disable incremental recursion using the --no-inc-recursive option. 
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