[Cohen]

Well, a pre-battle bombardment could be a good way to deal with war engines.
Historically before the campal battle the armies usually stay camped for some days, making probe attack and such.
This could be a chance for war engines to deal damage to enemy, and if we want to consider even the use of light infantry and cavalry to skirmish and to make hit and run attacks on the enemy, supply depots and such.

Otherwise war/siege engines could deal damage to besiegers, plus the bonus of sieging. I mean the catapults shooting inside the fortress and on the walls could cause losses to defenders, and vice-versa defending siege engines could deal damage to besiegers.

All stuff should be done off-combat.

If you lose the battle you're lose your siege weapons .