So really this is a weird bug I'm having. I've tried and checked and just can't find what's wrong with it. Basically there's an inventory with 29 slots, 27 are storage slots, 1 is a "foodprint" (blueprint) slot, and the final is the output slot. When the entity updates it's supposed to check if the item in the foodprint can be crafted (So if the foodprint is bread it needs 3 wheat in the storage slots) and if it can, it will take 3 wheat, and put one bread in the output slot. However after the first time the item is crafted per game instance (So you restart and it works again) the recipe outputs stack size goes down to 0 for some reason and any bread put into the output slot is fake and upon trying to eat it, it disappears. Here's the code, any help would be nice

 

@Override public void updateEntity() {
	if (this.worldObj.isRemote) return;
	if (ticksUntilCheck > 0) {
		ticksUntilCheck --;
		return;
	} else {
		if (!recipesCached) {
			if (getStackInSlot(27) != null) {
				ItemStack stack = getStackInSlot(27);
				if (stack.getItem() instanceof ItemFoodprint) {
					ItemStack stored = new ItemStack(((ItemFoodprint) stack.getItem()).getStoredItem(stack));
					for (Object obj : CraftingManager.getInstance().getRecipeList()) {
						if (obj instanceof ShapedRecipes) {
							ShapedRecipes recipe = (ShapedRecipes) obj;
							if (recipe.getRecipeOutput().getItem().equals(stored.getItem())) {
								cachedRecipes.add(new ShapelessRecipes(recipe.getRecipeOutput().copy(), Lists.newArrayList(recipe.recipeItems)));
							}
						} else if (obj instanceof ShapelessRecipes) {
							ShapelessRecipes recipe = (ShapelessRecipes) obj;
							if (recipe.getRecipeOutput().getItem().equals(stored.getItem())) {
								cachedRecipes.add(new ShapelessRecipes(recipe.getRecipeOutput().copy(), Lists.newArrayList(recipe.recipeItems)));
							}
						}
					}
					recipesCached = true;
				}
			}
		}

		ticksUntilCheck = 10;
		if (getStackInSlot(27) == null) return;
		ItemStack stack = getStackInSlot(27);
		if (!(stack.getItem() instanceof ItemFoodprint)) return;
		ItemFoodprint print = (ItemFoodprint) stack.getItem();
		if (print.isBlank(stack)) return;
		Item foodStored = print.getStoredItem(stack);
		if (getStackInSlot(28) != null) {
			if (getStackInSlot(28).getItem() != foodStored) return;
		}

		recipescan: for (ShapelessRecipes reciperaw : cachedRecipes) {
			ShapelessRecipes recipe = new ShapelessRecipes(reciperaw.getRecipeOutput().copy(), Lists.newArrayList(reciperaw.recipeItems));
			if (getStackInSlot(28) != null) {
				if (getStackInSlot(28).stackSize + recipe.getRecipeOutput().stackSize > getStackInSlot(28).getMaxStackSize()) continue recipescan;
			}
			HashMap<Item, Integer> reqItems = new HashMap<Item, Integer>();
			for (Object obj : recipe.recipeItems) {
				if (obj instanceof ItemStack) {
					ItemStack ing = (ItemStack) obj;
					if (reqItems.containsKey(ing.getItem())) {
						reqItems.put(ing.getItem(), reqItems.get(ing.getItem()) + 1);
					} else {
						reqItems.put(ing.getItem(), 1);
					}
				}
			}
			HashMap<Item, Integer> storedItems = new HashMap<Item, Integer>();
			slotscan: for (int slot = 0; slot < 27; slot ++) {
				if (inventory[slot] == null) continue slotscan;
				Item storedItem = inventory[slot].getItem();
				if (storedItems.containsKey(storedItem)) {
					storedItems.put(storedItem, storedItems.get(storedItem) + inventory[slot].stackSize);
				} else {
					storedItems.put(storedItem, inventory[slot].stackSize);
				}
			}
			for (Item item : reqItems.keySet()) {
				if (!storedItems.containsKey(item)) continue recipescan;
				if (storedItems.get(item) < reqItems.get(item)) continue recipescan;
			}
			slotscan: for (int slot = 0; slot < 27; slot ++) {
				if (this.inventory[slot] == null) continue slotscan;
				if (reqItems.containsKey(this.inventory[slot].getItem())) {
					int toTake = reqItems.get(this.inventory[slot].getItem());
					if (toTake <= this.inventory[slot].stackSize) {
						reqItems.remove(this.inventory[slot].getItem());
						this.inventory[slot].stackSize -= toTake;
						if (this.inventory[slot].stackSize == 0) this.inventory[slot] = null;
					} else {
						int newToTake = toTake - this.inventory[slot].stackSize;
						reqItems.put(this.inventory[slot].getItem(), newToTake);
						this.inventory[slot] = null;
					}
				}
			}
			if (this.inventory[28] == null) {
				this.inventory[28] = recipe.getRecipeOutput();
			} else {
				this.inventory[28].stackSize = this.inventory[28].stackSize + recipe.getRecipeOutput().stackSize;
			}
			break recipescan;
		}
	}
}

That's why when I cache the recipe and start the recipe scan loop I create a new ShapelessRecipes with what should be a copy

 

recipescan: for (ShapelessRecipes reciperaw : cachedRecipes) {
ShapelessRecipes recipe = new ShapelessRecipes(reciperaw.getRecipeOutput().copy(), Lists.newArrayList(reciperaw.recipeItems));

 

Shouldn't that be enough as long as I just use recipe everywhere and not reciperaw, or can you point out where I've messed it up

Well that appears to have fixed it, thanks!