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Wait, wait, wait... Which way are you going?

2006 Mac Pro to a 2009 Mac Pro, right?

Leave the installation that is on the new Mac Pro alone, migrate your data, and then wipe your old Mac Pro's disks if you were going to put them in your new Mac Pro. The 10.5.6 that is already on there will be fine to leave alone.

If you're going the other way for whatever reason, I don't know what to say about what to do, so I hope you're moving forward.

Yes, I am moving from the 2006 to the 2009 model. However, since I need a RAID setup, I will remove the stock drive and replace it with 4 * 1 TB disks. Those are already in my 2006 model so I was hoping I could just swap them over.
 
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