This has happened twice now...
On the crystal isles map, I was building a small shelter, one day I log in to find everything but the foundations just gone. Walls, storage box, bed, just disappeared.
Started building a larger wood base. Few real days into playing and EVERYthing is gone including my 2 tamed dilos. I'm in a low danger area and there are no aggressive dinos anywhere nearby.
I do not have structure decay on. Only mod is structures plus.