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I had some hard drive problems a little while ago, so installed a new drive system, and restored data from my Time Machine Backup. However, the mount point is very different from the one originally backed up.

Right now I have a 6 TB backup drive, with 1.6 TB free. I have 4 TB's to backup to it, most of which is already on the backup drive, just mapped to a different folder/volume.

I'm quite comfortable using the shell or whatever, I'm just getting permission problems or 'operation not permitted' when trying to move the folders to an existing tree, or to even create a symlink.

Hopefully I don't need to dump my old backup data in order to continue backing up.

Is there a way I restructure the backup folders on the Time Machine drive, so I don't lose my backups from before this restore point?

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Restructuring the files manually isn't a very easy or practical solution. Due to the hard links used to store the files and the data structures and metadata involved for Time Machine to track which files have changes, it would be better to live with the change.

You can enter Time Machine and delete entire backups or manually delete files or entire snapshots. If you do nothing, you will have two copies of some files where you would have had one had the normal compression of files being stored in the same path are unchanged on the backup when the file does not change. Once Time Machine sees that you don't have enough space to hold the next backup (as it estimates each backup need before starting) it will then do the clean up by time for you.

Technically, the system has locked the backups into a special state where even root has to disable the protections to then delete files. It's much better to use tmutil to delete entire snapshots (or a range of them systematically) or the normal UI to delete all backups of a folder or a file.

You could also just put that drive on a shelf and start with a new one. This does add extra cost (well a lot of cost for 6 TB of disk) but you won't have to lose backup history. If the files are truly duplicated, just let Time Machine clear enough space to accommodate the next backup and you should be clear. The risk is that the deletion happens before the backup starts, and there is a short window where a bit more than 4 TB of data was deleted, and you haven't made a new backup copy of the files - they will only exist on the source and a failure during that next backup could cause you data loss.

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Thanks for your response. Do you know how I can get the TM backup to purge the old files? Right now when I try to backup the new mount points, it simply says there isn't enough free space. (I don't want to buy new hard drives right now.) (I do have a separate backup set, so I can keep that one as spare.) –  SilicaGel Nov 30 '12 at 16:56
    
I edited my answer to link to an question here on manually cleaning. Again, you don't need to do anything unless Time Machine refuses to start a backup, it should just keep backing up and do the cleaning automatically as it needs more space. –  bmike Nov 30 '12 at 17:10
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Thanks, I used the 'cog' to remove all copies of a given folder (by date didn't work, as I could see anything older than the last few weeks for some reason.) –  SilicaGel Nov 30 '12 at 17:59
    
The cog gets frequent use by me. Especially on clients with Entourage / Outlook - large monolithic database files that you want a short retention, but over time take tons of space. It's great to purge all backups of a certain folder or tree when you don't want to just retire an old drive and let it sit on a shelf as a historical back up. –  bmike Nov 30 '12 at 18:05
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