first mount and make sure you know where the hardrive is with df or mount.
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mount /dev/hda1 /hdd1
mount /dev/hda2 /hdd2
or
mount /dev/hdc1 /hdd1
mount /dev/hdc2 /hdd2
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then cd /hdd1 cd /hdd2 and make a directory in each
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mkdir .sys
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then
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cp /mnt/cf/hdd1sys/* /hdd1/.sys
cp /mnt/cf/hdd2sys/* /hdd2/.sys
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after you are done, cd into the directory and see if you can see the files that each hdd1sys and hdd2sys making sure if its in there. sometimes you may need to play with it cuz its a bit buggy. I'm not sure if it's me or my commands or what. but you will struggle a bit. if you cd int /hdd1 and hdd2, you will find lost and found but make sure you see .sys files(remember directory is invisible.) if you still cant get the files going, su at the start even though your already root.