All bases change ownership into "default" (determined during map). That may or may not result in the base below you changing ownership.
If you are still in air when the arena resets ("host connection lost"), your current sortie doesn't count for score purposes. You will not lose any perk points. (Of course, you won't gain any from kills made during that sortie too). Your kills made during this sortie are not lost for for stats purposes, as the stats database is updated in real-time during the sortie.
So if you find yourself deep in enemy territory in a 262 - just stay alive until the reset boots you from arena.
IF you have been part of the winning country for at least 12 hours before the reset (and played during that period) you will get the perks (25 per category) for winning the war. You don't have to be online the very moment the war is actually won.