I must be a fool to report this because it saves me loads of gems Maybe it's even good behaviour...
When a mine is exhausted the player can delete the "mine". I mean the mine not the mason! After I tell my Geologist to discover stone, he finds the stone vein that was exhausted minutes ago. No need to refill the mine, just let it run dry and rediscover it
I didn't had time to test this for copper, marble, iron etc...