Excess wounds inflicted against war machines are never carried through onto other war machines, not even where they are fighting in the same battery.
In this respect war machines continue to fight as if they were single models, even when fighting in batteries. However, they still take Break and psychology tests as one unit, will flee and pursue as one unit, and in other respects are treated as a unit. Note that this is consistent with the rules which apply to squadrons of chariots, and so shouldn't be too hard to remember.