I know I promised the config would auto-update but just this once you have to delete the config.yml and let it regenerate.

New Config Option:

• disable_during_war:
  • default: true
  • If set to false, players can still fly in their town while war is active.
  • This prevents players starting to fly while the Towny war event is active. Until I add a war start event to Towny I cannot disable people already flying. This will happen eventually.