Yes, you can delete your mission files without doing any harm to the mod or the game itself. If you're going to delete a mission, make sure to delete the corresponding .mach-files as well (beginning with the same number as the mission). Usually these won't be needed anymore with one exception: if you've made a mistake numbering your missions and fixed this issue by assigning a new number to the problematic mission, then this particular mission will still need the .mach-files beginning with the old number. If you delete these .mach-files,then the mission won't work anymore.