Log into a root shell
It's a mix up of multiple things. It simply means, login into a shell and then switch to root user or alternatively, directly login as the root user. For Android, you can login from a remote shell using adb shell command. It automatically logins as user 2000. Alternatively, use a terminal emulator app and it would automatically login using its own UID. In both the cases, don't bother about the term "log in".
Switch to root user using su.
sqlite3 is a command-line tool to interface with SQLite databases. Stock Android doesn't come with it.
That command does nothing more than attaching the database naver_line located under /data/data/jp.naver.line.android/databases/ to sqlite3 so that latter can do its work on it.
delete from setting;
I don't have that app or its backup but the command indicates that there is a table named setting in the said database. That command would delete all the data available in that table.
It would disconnect the database and exit from the sqlite3 tool.
I don't know whether those commands would achieve anything or not, so take this solution as a partial answer only.