I try to install update for XCode and high sierra 10.13.2
However, there is phantom process which I cannot restart.
All the sql-developer process is gone but somehow it thinks its still there.
You can force kill the process through terminal killall SQLDeveloper
1.
Then proceed to restart
To get to your original objective which I interpreted as 'restarting your macOS'.
Related: macOS - Mac App SQLDeveloper stuck in Dock after application closed, Process killed - Ask Different
1Forcefully killing processes can have unintended side-effects.