Well, if they are allowed to die earlier on, then yeah it'd screw things up. Overlooked that before.
Another method is to use a proxy, and have the directive event not check for the docking at all but for something else that is more easily controlled. Say, the destruction of invisible fighters in a wing named with invisible characters that sit 200.000 km outside the play area. Then, as each transport undocks, you can trigger changes in the directive count by self destructing the fighters. It's an ugly hack but it'll do the job if you insist on having a count in the directive.