On a new world with no mods, I get the same behavior. We never killed Eikthyr (although we got a club-wielding Troll to mine us some Tin and Copper to get our pickaxes). This happened before we took on the Elder.

I've also noticed that the Skeletons at Burial Chambers now respawn. This used to not happen on my other worlds (though I was using Valheim Plus on most of those). I just assumed that it was an intentional change. (I haven't really sat down to play in almost a year.)