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This process will require some time. Prior to start you'll basically need to backup some of the contents from your old MySQL fedora3 database as well as the some sub-directories from the old Fedora data repository (objectStore and  datastreamStore), perform a fresh installation of Fedora 3.8.1 as instructed on milestone1, test that everything works fine all way through milestone 6, then migrate those backup components onto the new installation.

So far we have no reasons to believe this process would not work for updates of Fedora 3.6+ and prior to 3.8.1