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My method kali 2017.1
Open rufus, insert your usb drive and select the ISO image to use
You are done! Restart your computer and set your usb drive as a boot device.
Select persistence and start
Type gparted in a terminal window
Select usb disk unallocated block
Create new Partition
Create as: Primary Partition
File system: ext4
Label: persistence
Select Apply All Operations
Open terminal window
fdisk -l
see sda2 ,sdb2 or sdc2 your usb and edit code (no change other)
mkdir -p /mnt/KALI
mount /dev/sdb3 /mnt/KALI
echo "/ union" > /mnt/KALI/persistence.conf
umount /mnt/KALI
and reboot
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Thank you, this procedure worked nicely for me. All my settings are now persistent EXCEPT I am unable to change the root password.