AmigaOS does not do any file locking on the boot partition. You can copy the running system to another HDD. Simply open a shell window and enter
copy xdh0: ydh0: all clone
where xdh0 is the installed source partition and ydh0 is the empty destination partition.
Whether a partition is bootable or not is decided in the partitioning tool (e.g. HDToolbox). There are no files which make a system bootable. You can even boot from an empty partition.
