The object of type 'Transform' has been destroyed but you are still trying to access it.

I have no idea whats wrong. it should work perfectly!

    var ShootFromHere : Transform;
var Flame : Transform;
var speed = 2.0;
var length = 10.0;
private var del = false;
private var water;
private var news;

function Update () {
makeFire();
}

function makeFire() {
if (Input.GetMouseButtonDown(0)) {
water = Instantiate(Flame, ShootFromHere.position, transform.rotation);
news = true;
}
else if (Input.GetMouseButtonUp(0)) {
if(news){
news = false;
water.particleEmitter.minEmission = 0.0;
water.particleEmitter.maxEmission = 0.0;
yield WaitForSeconds (15);
Destroy(water.gameObject);
}
else{
//This prevents the error from the object already being deleted.
}
}

//Check for existence, then move it to ShootFromHere
if (GameObject.Find("large flames(Clone)") != null)
{
    water.position = ShootFromHere.position;
    water.rotation = transform.rotation;
}

}

Just a guess, but have you set the ParticleEmmitter to Auto-Destroy? Then it will destroy itself once it stops emitting, so you don't need/can't do this manually.