Here’s what I ended up doing:

When the SSD arrived, I put it in the 2nd slot. Then, I booted Ubuntu in a Live USB and created the same partition layout in the new disk with parted.

1. Create the EFI partition and give it the same size
2. Do the same for the ext4 boot partition
3. Create a btrfs partition and give it the remaining size.
4. Encrypt this new partition with cryptsetup and mount it with the option luksOpen of cryptsetup.

Next thing was mounting the partitions of the old drive. And now, to clone the disk I first tried with brtfs-clone but as the size of what first were 220 GB increased to 260 GB, I tried just using btrfs send from the old disk and piping it to btrfs receive to the new disk. However the size didn’t change and still was 260GB, no idea why. I didn’t use dd because some comments recommended btrfs send/receive as it doesn’t copy the whole partition including empty space.

Once that was done I copied the /boot/efi and /boot partitions using cp and changed the uuids in /etc/fstab and /etc/crypttab to match the new partitions UUIDs (to know which UUID was each partition, I just used blkid and grep’ed the type of partition. For instance if I was looking for the new partition to replace the one with UUID a1b2c3, I would just use blkid | grep a1b2c3 and if it said it was a crypto partition, then blkid | grep crypto). Finally I deleted the Microsoft folder from /boot/efi as I would only use that disk for Linux.

So then I tried booting from that disk (and removed the other) but Grub was a mess - it just showed the command line. After some (stressful) hours, I found out that it was because Grub itself when first installed saves the UUID of the disk where the config is and searches for it there - so it was not using the config in the new drive.

Again, booted Ubuntu and mounted the new drive partitions. There I tried to just reinstall Grub in the boot partition but it seemed impossible because of some weird errors. So I just changed the UUIDs in Grub related files such as /boot/grub/grub.cfg and /etc/default/grub.

Tried booting again but as noticed earlier Grub was not loading the config file I edited, it was still trying to use the old one in the old drive which was removed and had the original UUIDs. Maybe just changing the UUIDs there would have done the trick but I didn’t try.

It was in that moment that I discovered the existence of configfile - a command that can be used from Grub’s shell to boot with the specified config file. Then I used configfile disk_and_path_to_grubcfg and bang! The OS selection screen appeared. At that time I had already put the old disk in the other slot as I thought everything was solved.

To my surprise, when I selected to boot fedora and typed my password to decrypt the drive, I booted to Fedora in the old drive! How could that be, if I really made sure that I was booting Grub from the new disk? So now the problem was that I was booting Grub (manually with configfile) from the new disk but the OS I was booting was in the old one.

After some time researching, the culprit was that while I changed the UUIDs in the grub.cfg config file, Fedora doesn’t add its kernel entries to that file but to the /boot/loader/entries directory. And there were the files I had to modify (just replacing the old UUIDs). One reboot (maybe also update-grub to update Grub config) and that was it, solved.

However there was one more thing to do. As I didn’t want to use the configfile command every time I boot, I just reinstalled grub.

So that was it. Hope it is useful for anyone who needs to do the same. Although the story doesn’t end there, because the new drive turned out to be defective and I had to order a new one to which I dd’ed (not going through all that again). You live and you learn!