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I would effectively like to switch from a case-sensitive journaled filesystem to that of a case-insensitive journaled filesystem. Booting into Lion's recovery allows me to format the drive as I wish, however, no matter what I choose Time Machine will always reformat it as a case-sensitive journaled filesystem (which makes sense). My question is, how can I make this switch?

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Do you get an error when you set up a new Lion that is case insensitive and attempt to restore from the case-sensitive backup? (or how is the system forcing the switch back). Migration assistant might be more friendly if you want to set up the mac as you wish and only introduce the data at a later date - once the filesystem case sensitivity is firmly established – bmike♦ Sep 22 '11 at 17:21

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The correct answer (after several days of experimentation) was to remove all ambiguously named files that would have a conflict. Then using another admin user, restore the original user using migration assistant. If you don't remove ambiguously named files, migration assistant will move what it can and then fail at some point giving no indication that it actually failed. You'll be without data and you won't know what.

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What do you mean by ambiguously named files? I'm having the same problem. I just loaded everything backup after formatting and using Time Machine and cannot install certain programs because of the case sensitive format. – user17520 Jan 21 '12 at 3:19
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You can restore from TimeMachine manually by opening Terminal.app and using cp to copy the latest backup back to your main drive. Taking care of all the permission and metadata issues isn't for the faint of heart though (which makes it a bit difficult to provide a specific answer as well).

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