OH MY GOOOOOOD!!!
Clannad deleted all my endings! It turns out that it was not finished downloading, I had gone through 33 playthroughs and one After Story unfinished. Aww man! I had gotten nearly 100%, then boop, when I booted it up, WHAM! ALL DEAD ALL DEAD.
(The version I got was the fan translation from some time ago, not the official one… so sad. ;-; )