Thing is, without evidence to the contrary you are on thin ice and they know it.
Its like when they damage your wheels or paintwork when its in the workshop (very common), you need to have photos showing the condition on arrival or a walk around with a damage sheet that is signed or you won't be getting anywhere.
Probably in this case if you can get them to admit the current water ingress is caused by the missing hatch then you can extrapolate that the previous was identical therefore the root cause of both was identical and ask them why the problem was not identified previously and resolved...
