Not sure I follow you so let me give an example.
Suppse Cancer wing is set to have 5 waves. If the freighter they are after is destroyed after 2 waves are gone the enemy stop sending any more waves but you want the current wave to stick around and fight Alpha.
How can you set that up so that the waves stop coming immediately after the freighter is destroyed but the current wave (whatever it is) sticks around to fight?
EDIT : No sooner do I post this than I come up with a smarter solution. Give them orders to depart but break their warp drives

That should take care of the problem

Assuming of course that breaking the warp drive on Cancer 1 in wave 1 breaks it on Cancer 9 in wave 3 etc.
Hmmmm. This still requires some tinkering
