You should quit the engine using AppleScript, not kill -9 (which basically just stops it instantly with no ability to cleanly exit). kill -9 will almost certainly lead to corruptions of things like the variables database if you do it enough and get unlucky.
Starting the engine is best done by specifying the full path to the Keyboard Maestro Engine to ensure the correct version is run if you have an old version of Keyboard Maestro on your Mac (which you should generally avoid) by using the open shell command.
A better question though is why do you have to quit & relaunch the Keyboard Maestro Engine multiple times a day. That is decidedly not normal.