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 /data/data/jp.naver.line.android/databases/naver_line
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.
.quit
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.