You can check on the map, maybe it's underground in some dungeon or cave. You can switch the teleport map to underground by clicking the button in the lower right corner if I remember well.

If you dropped it somehow you can load older game saves, find the the area where you lost it and hopefully narrow the search. Maybe it's on the ground or maybe you accidentally put it in a chest.

On the other hand, if you find some more magnesite ore you can complete one of the early quests and get 2 more stones which should be enough (unless you already had 3 and lost all of them).

PS Based on personal observations the loot will stay there forever or until you pick it, whichever comes first.