Ki Ryn said:And when you target a flask of holy water with invisibility, does only the flask turn invisible, or is both the flask AND the water inside affected? Silence can target an object. A flask of holy water is an object. Heck, you could even target the water without targeting the flask if you wanted too (freeze the water, target the ice cube, melt the water back into the flask).
There isn't an easy way to lawyer your way out of it, you just have to admit it's silly and disallow it on those grounds.
The water is invisible BECAUSE it is inside the flask. Pour the water out and it becomes visible. And, as others have mentioned, break the flask and it possibly breaks the magical effect on the flask.
I don't have my books here, but any spell that requires that you be able to see the target would require that the flask in question be clear or translucent, or the water could not be targetted, as you would be unable to see it.