Applies to Yosemite Server Backup 8.1 and newer running on Linux.
Yes, Yosemite Server Backup does backup hard links. However, it is important to understand how it processes them. During a backup, when the first instance of a hard link is found the source data is backed up. The information on this hard link is in turn added to a table that Yosemite uses to track these. Each time after the first time Yosemite encounters a hard link that points to the same source data it will back up a reference pointer but not the source data. This allows us to ensure that the source data is only backed up once and not duplicated throughout the file structure for each hard link. It also ensures that the source data is captured on each backup and does not only back up links to it.
On restore, the source data is only restored when the first instance of a hard link that was backed up is restored. All other hard links that pointed to that data are recreated but the source data is not restored. This ensures that if a restore of multiple versions is done that the most recent copy of the data is kept and that each selected hard link pointing to that data is recreated. The only problem here is that if during the restore the hard link that was used to collect the source data is not selected and only the duplicate hard links are selected then the source data will not get restored.
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