I had something similar happen to me. I almost had all skills unlocked except for the last cooking skill and I had just reached level 11 in mining, so I went to mine the coal deposits (with the acumulator) and when I exit from the mine exit below the forge almost everything outside the cave was reset to how it was at the start, all fires weren't lit anymore with the matching NPC's gone, all my crates were gone. Instead I could find my crates that were inside the mine on the surface. Lily's and Pierre's quest was still finished. For the inside of the moth mine and the mine everthing stayed as it was including crates. I could get a new ember heart from solving the standing stones puzzle again, so I relit the fire at Kings and talked to King and his quest was also still finished. Very much enjoyed the game.