I have had this happen to my manually saved games twice in the last 2 days. I am setting up Skyrim for VR and mods etc so have been loading in and out to test FPS and make sure nothings broken.
I have no idea what is causing this. Very frustrating though as I have to keep going back to my initial autosave, which is immediately after character creation, and watch the dragon swooping in again.
*This is before any mods installed, so nothing to do with mods.