Similar issue. I had a game crash when entering a Better Ruins ruin. When I restarted the game, the ruin was nowhere to be found, I was a few blocks underground in a modded village. The elk was nowhere to be found even after retracing my route back home in creative while blowing the flute and watching a Block Overlay scan for tamed elks. The marker is at home in the usual "elk parking place". Spawning a new elk doesn't work - it doesn't accept a medallion, so the original is probably *somewhere* alive.