Linux

Set up a proper backup system for your server. I like to use borg. Just to be safe, make a copy of your drive as well (like full disk rsync). Then do a clean install and restore as if your drive had failed. If your backups missed anything, you will now know and can fix your backup system and can still recover from your rsync'd drive.

You might also want to take this opportunity to start administering your server with code, like using ansible or other remote provisioning tools. This makes your system configuration reproducible so that you only really need to back up a few kinds of data like media files or databases.

I dont know if this would be applicable for your use case.

But in gentoo one of the recommended ways to backup your system is rsync. Rsync is single threaded, but keeps all softlinks and hardlinks aswell as accepting an exclude list for directorys you want rsync to ignore. I have recovered from some pretty big dumb dumb moments and have used rsync to build packages on my threadripper and syncing them to lower power devices like my laptop and raspi. And they work pretty well!

If you do decide to go with rsync you can use "rsync -aP (from directory) (to directory)" the "a" stands for archive this keeps all permissons, softlinks and hardlinks. The P stands for a progress bar, so you can see how its going. Another benefit of rsync is you can start copying and stop and start and it will only SYNC over what isnt new or modified. After the files are synced over you need to edit your fstab (its af file where you computer mounts your disks) and grub-mk-config. If not re-install grub

Hope this helps

If you don't want to reinstall the OS, you can probably use Clonezilla: https://clonezilla.org/show-live-doc-content.php?topic=clonezilla-live/doc/03_Disk_to_disk_clone

Maybe you need to update the drive ids for your bootloader (grub) afterwards, not sure about that.

Edit: Maybe the advanced "-g auto" option does that for you.

dd then resize the fs?

Edit: one caveat here I forgot: if your fstab is using UUIDs, you're going to have to update that, since the new drive won't be the same UUID because, well, it's not the same drive.

When I've needed to transfer data over to a new disk, I've used gparted from a live usb to copy/paste partitions directly. Once that's done, you'll probably need to update /etc/fstab to point to the new drives and run update-grub (assuming you are using grub) to update the bootloader config.

If you're using LVM, ZFS, or Btrfs then you can use their features and tooling to migrate data from one disk to the other, assuming you're able to connect both at the same time.

I've done this online with btrfs several times now and it's quite painless, admittedly only for self hosted stuff.