Six things in Graveyard Keeper 2 come back after you harvest them. Everything else you break is gone from that save for good, and the game never tells you which is which.
That matters more than it sounds. Clearing scenery for materials feels like tidying up, and on most of the map it is quietly spending something you cannot get again.
Six things come back, and that is the whole list
A sand pit, a clay spot, a copper vein, a stone source, a marble source and the upgraded garden well all refill themselves moments after you empty them. Those six are the game’s renewable supply and there is nothing else in it.
The two you meet first are the cheapest. A sand pit gives four 
Sand and wants Building three, a clay spot gives four 
Clay and wants Building two, and both are dug with a shovel in hand even though neither measures the Farming track a 
Bronze Shovel feeds.
A copper vein is the one to know about. It is the only place 
Copper Nugget comes from anywhere, it asks for Smithing two, and it hands over three a harvest with the Miner perk adding a fourth. Because it refills, copper is the one metal you can never run out of.
There is a stone source and a marble source that refill, at Building four and Building seven, and there are stones and marble scattered across the map that do not. They look alike and they are not. The scattered ones give between one and four 
Stone once and then the space where they stood is empty for the rest of the save.
Iron is two harvests and then nothing
An iron boulder is worth exactly two visits. Mine it once for three 
Iron Ore, and what is left behind is a second boulder worth another three, and mining that one leaves bare ground.
Six ore a boulder, or eight if you have taken Miner. Every boulder asks Smithing three and makes you hold a pickaxe, which is the trap the Iron Ore page covers: a better 
Bronze Pickaxe raises Building and does nothing for the gate in front of you.
There is no second iron anywhere. However many boulders the map holds is how much iron the save contains, so the Miner perk is worth taking before you start rather than after.
A tree is two harvests, a bush is one
Chopping a tree leaves a stump, and the stump is a second harvest rather than debris. The tree gives 
Log and sticks to an 
Bronze Axe, the stump gives more to a shovel, and digging it out leaves nothing behind.
Bushes are worse because they look untouched afterward. Pick a berry bush and it becomes an empty bush of the same shape standing in the same place, so a patch you have already stripped is easy to walk back to and hard to tell apart. 
Berry does not grow back on it.
Of everything in the world you can break, only those six refill. Trees, stumps, bushes, scattered stones, iron boulders, barrels and rubble are all one visit or two and then gone, and no season or quest brings any of them back.
Break scenery because you want the space or you need the material today, never because it will be there again next week.
What each of the six costs you
Two hundred and six things in the world can be broken for materials and nine of them renew, which is the six kinds counting the two wells and the two pits that have a zombie-friendly twin. The mastery each one asks for is what decides the order you get them in.
Clay and copper open first at mastery two, sand at three, the stone source at four and the marble source at seven, which is deep enough that marble stays a late material whatever else you have built. Clay and sand read Building, copper reads Smithing, and all three want a tool that feeds neither.
The garden well is the odd one and the generous one. It asks for no mastery at all, the first tier gives ten 
Water a draw and the upgrade doubles that to twenty, and both refill, so water is the one material that is free from the first day to the last.
What to do about it
Treat the six as your supply and everything else as a windfall. Sand, clay and copper cost nothing but energy and never run down, so a job that can be done with those three is a job you can repeat forever.
Iron and marble are the two to ration, because both are finite on the map and both sit behind mastery you will not have early. Take Miner before you clear the iron, since the extra ore only applies to boulders you have not mined yet.
And 
Coal has no source in the world at all. Nothing you break drops it, so every piece you ever own is made rather than found, which catches people who go looking for a coal seam that does not exist.
Graveyard Keeper 2 resource respawn FAQ
Do resources respawn in Graveyard Keeper 2?
Six do. Sand pits, clay spots, copper veins, the stone source, the marble source and the upgraded garden well all refill seconds after you empty them. Everything else in the world is gone once you have taken it.
Do trees grow back?
No. A tree gives one harvest, the stump it leaves gives a second, and digging the stump out leaves bare ground that stays bare. No tree in the world regrows.
Does iron ore respawn?
No, and iron is the tightest material in the game. A boulder is worth two harvests of three Iron Ore each, six in total or eight with the Miner perk, and then it is gone. However many boulders your map holds is all the iron the save will ever have.
Can you run out of stone?
You can run out of the stones lying around the map, which give one to four each and never return. The stone source that refills is a different object and asks for Building four, so early on the scattered ones are all you have and they are finite.
Do berry bushes regrow?
No. A picked bush turns into an empty bush of the same shape in the same spot, which is why stripped patches are easy to revisit by mistake. The berries do not come back.
Where do you find coal?
Nowhere. No object in the world drops coal, so all of it is crafted rather than gathered. Looking for a coal deposit is the mistake; building what makes it is the answer.
