Ah yes, I forgot that the mines are loaded separately from the main map. But are they flooded only after the party leaves the map? I remember them being flooded while my party is still in them (spoiler, mark to show: right after the encounter with the Conduit). If so, a pyramid could still lie around in the flooded part.
I heard about the enemies that may teleport you into lava, but fortunately, that never happened on our single playthrough in normal difficulty.