Your confusion seems to stem from misunderstanding what is looping and resetting.
The war is not what is being reset - it is the personal timelines of Rita and then Cage. Their looping is because they initially die after being contaminated with some of the aliens' blood and they are grafted the looping ability.
The aliens must have either evolved or developed the ability to loop their own timelines on death so that they can adapt and learn to overcome whatever killed them initially. So, there are actually multiple timelines being reset all over the place as aliens die and reset.
All in all - it's probably not a good idea to get much further into the physical and metaphysical ramifications, because it's apt to give even Doctor Who a nasty headache...