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1. Use rsync while the system is running in the normal runlevel. Logout all users first and do that from the root account so that the data in /home will not be altered during the copy. Just for safety.
2. this makes no sense, why would you copy the /-partition to the /boot-partition? If you mean /new_root instead of /new_boot the do it from a live-medium, the system should not be running.
If rhe system is running you will have many files that may change, like log-files or a running database. Therefore it is recommended to copy from a not running system to avoid inconsistencies. It is not a necessity, but recommended. You cam also do it from a running system when you exclude such files and the files generated from a running kernel like the /proc and /sys trees.