I would clone the second disk to the new disk (with gparted for instance) an then resize the partion to fit the disk. This way it would be a simple disk swap without needing to do anything else.
PS: I think simply copying the files will go wrong with the hard links.
Sorry I wanted bit to fast. Clonezilla will clone disk including huid (which can mess things up is you keep both in the pc). But then you can boot clonezilla, clone disk (has a flag -k1 for resizing partitions), remove the old disk, and should work without changing anything else. If you want to change the settings anyway, there are more options like DD. For clonezilla instructions, see https://clonezilla.org/fine-print-live-doc.php?path=./clonezilla-live/doc/03_Disk_to_disk_clone/00-prepare-clonezilla-live.doc#00-prepare-clonezilla-live.doc