Honest Question:

Isn't this something we can expect to happen in an Early Access game?

As the game is in development, deleted progress may be pretty common. Not sure about Valheim, specifically, but other games in the genre regularly go through this.

In those games, though, if you want to keep going in your world, you need to roll back to the most recent version that worked for your world. AND THEN turn off updates so you can stay on that version.

I'm not sure that'll fix your issue, but it might.