Re: Will using a cloned boot drive cause problems with my bootloader?
I would suggest copy instaed of clone. You create the partitions on the SSD first (the partitions will not have the same size as on the HDD I assume since SSDs are quite smaller) instead of cloning them.
With this step you avoid having duplicate UUIDs even if both the ssd and hdd stay in the computer.
I would copy windows partition from ubuntu live mode too, although ntfs doesn't use ownership and permissions the way linux does, but still it doesn't hurt I think. Use the cp -ax to keep ownership and permissions which is a must for the ubuntu partitions.
After you have copied all, I think windows should work fine. For ubuntu you will have to adjust the UUIDs in /etc/fstab (on the ssd of course) and it's better to enter the installation with chroot to do update initramfs and grub2 reinstall. That makes sure it "gets" the idea it's on a new disk.
If it fails, you still have your original data on the hdd. Never delete it until you see things are working with the ssd for sure.
Darko.
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Ubuntu 18.04 LTS 64bit
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