Running the uninstaller might clean up some things better, of course you could always do a test to see for yourself.
But technically, it should but the uninstaller is here: http://download.macromedia.com/get/flashplayer/current/support/uninstall_flash_player.exe
I would make sure that all flash dependent processes are closed as your jobs might fail. There are a few out there.
There is no need to re-boot if all processes are killed