As per How do I restart Unity? But I guess
unity --replace would start the 3D variant.
unity-2d has some of its own processes and some processes that derive from unity (unity-2d uses unity libraries).
You can find these processes with:
This yields these (see the right-most tokens in the above command output):
Each of these can be individually stopped (and each will automatically restart) with:
So to kill them all, list them all in the above command:
Since it won't let me post a comment to answer the question, it's necessary to add an answer:
I can confirm that "killall unity-2d-panel" does in fact restart it, with no noticeable losses. I haven't tried the other ones though. (This command is necessary periodically if you're dealing with memory leaks like https://bugs.launchpad.net/ubuntu/+source/unity-2d/+bug/905854).