You don’t want to send your file repeatedly through Handbrake. Particularly not for something trivial like changing track titles. Because every time the quality will get worse.
Download and install MKVtoolnixGUI
and make yourself familiar with it.
For changing a whole series of files of the same makeup (e.g. a tv series), take a look at How to remove tag spam and set language in several MKV files at once
