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I have a MacBook Air with one SSD that unfortunately is formatted as journaled, case-sensitive.

I have an external HDD that I copied my whole start volume bootable to with the tool SuperDuper and it works fine.

When I format the SSD to the correct filesystem (journaled, not case-sensitive) it successfully formats it, but when I copy the data back with SuperDuper it transfers the old file system, too, rendering it useless.

How can I have the SSD with the system on it and the new filesystem?

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If you are familiar at all with Terminal you could try reading up on rsync and using that to copy stuff selectively over from your backup drive.

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