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Clonezilla runs lots of tasks after (and before)
dd
that are in the log file(s) on the live environment before you reboot. I haven't used it in a while, but I'm confident that one of the tasks is updating grubI did update grub via a chroot as one of my troubleshooting steps... So I don't think that was it either. I actually recall it saying something about skipping updating grub (because it was a GPT system without some special flag set I think).
I remember seeing it do something to the EFI stuff explicitly and I'm wondering if maybe that's where it did something I didn't.