If we surmise that it (whatever it is in the end) infected the entire population, killed (and then resurrected) a large portion - say 60-70% - then I'm sure that this would also have taken place within
the military - wouldn't it?
It's not like all military instalations are sealed airtight and the air filtered for the cause of what has been killing all the people.
And in this case a large portion of your supporting personnel (logistics, maintenance) as well as a sizable portion of your fighting force would also be sick-gone-resurrected
just like that (perhaps even in a matter of hours/days?), removing a large nummber of people with the training to fight the enemy as a cohesive force.