When you target a terror site or crashed UFO with a
ship, it does not disappear, giving you to get to it. If a terror
site is in the darkness, send Interceptors one after the other
to it. Hopefully, enough time will have passed to get the terror
or crash site in the daylight.
A simple way to avoid night time terror missions is knowing that
as long as the terror site is targeted, and whatever has it targeted
is moving towards it when the hour changes, it will stay there
forever. For example, if you need to buy yourself a few hours
before it is light out at the site, put your Skyranger on patrol.
A few minutes before the hour ends, target the terror site again.
Then as soon as the hour changes go back on patrol.