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I have an Asus Vivobook S15UN, which natively has an M2 ssd. I just installed an additional hdd (that I plan to use for backups), and after that the bios is, as I want, still setup to boot from the ssd. In fact at the very start, it offers me the usual choice whether to boot Windows or Ubuntu, each from it's own /dev/sda* partition. As I choose the usual Ubuntu, it shows the central logo and the 5 dots, for long, but it cannot finish regularly.

I think that until it thinks of disks as of ATA addresses, it finds the M2 at the expected place, but once it tries to mount the /dev/sda6 partition, it reaches the new empty disk instead, as the system partition is now named /dev/sdb6 instead...

Could it be that the new disk took the ATA0 index, making it /dev/sda?

From maintenace mode I verified that I can mount that partition, but how can I fix the boot configuration, or grub, or the mounts to make it boot regularly again?, without reinstalling the system?

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first of all, you need to make sure the second disk was not created using dd. Because if you did, dd cloned the UUID from the first drive. If you look into the grub bootloader, you will see the thing it points to is usually UUID of the disk. Example:

      search --no-floppy --fs-uuid --set=root  8062267c-ff0f-4cda-844a-f46c0abcdefg

this UUID can be seen on the list of disks printed by sudo blkid

if the second disk has the same UUID like the first one, the grub bootloader will use that to start.

If that's the case, use How do I change UUID of a disk to whatever I want? to change your second disk uuid

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