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Does adding the --removable flag to your grub-install command fix it?
Feel like a fool now. I was so focused on it being an encryption problem I forgot about that option
]]>Except I am keeping /boot on a usb stick (with the detached LUKS header)
It works brilliantly and the system will boot and decrypt the drive and mount the lvm partitions. It will also reboot happily many times, if I remove the usb drive during normal operation or during shutdown it also has no issues (as you'd expect). If however I shutdown the pc while the drive is disconnected, the drive will no longer read as bootable. At least until I rerun grub-install on it.
What am I missing here? Is it an artificial of luks2 encryption ?
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