NBT Disapears when Removing Crafting ItemStacks

Hey Guys, i have some problems,

I created some methods, that could handle every specific Recipe a minecraft Modder will ever need, maybe more. Everything works really fine, but my problem is, the Input Handler(The Handler, which Handles the Input Slots, so it removes the items after crafting) removes the Items not really good, I think its a problem between Server and Client syncing, it decreases the Item stacksize not correctly, and in fact, when it crafts with NBT, it deletes the NBT after crafting, but I really have no Idea how to fix this.

I cant show you the howl code, because you probably may need more than 5 hour so understand this.

public final ItemStack addInputSlotManager(ItemStack[] slots, int inputSlotArrayNumber){
	ItemStack itemstack = slots[inputSlotArrayNumber];
	boolean flag = false;
	if(getWorkingItemBasedRecipe(slots) != -1 && System.currentTimeMillis() -10 > lastCrafted && !(System.currentTimeMillis()-50 > lastCrafted)){

		for(int a = 0; a < slots.length; a++){
			if(a > slots.length - outPutSlots){
				if(slots[a] == null){
					flag = true;
					System.out.println("Yolo");
				}
			}		
		}
		if(flag && slots[inputSlotArrayNumber] != null){
			itemstack.stackSize -= itemBasedInputSlotDecrease[getWorkingItemBasedRecipe(slots)][inputSlotArrayNumber];
			if(itemstack.stackSize <= 0){
				return null;
			}
		}
	}else{
		if(getWorkingItemGroupBasedRecipe(slots) != -1){

			if(System.currentTimeMillis() -10 > lastCrafted){

				if(!(System.currentTimeMillis()-50 > lastCrafted)){

					for(int a = 0; a < slots.length; a++){
						if(a >= slots.length - 1){
							if(slots[a] == null){
								flag = true;
								System.out.println("yolo");
							}
						}		
					}
				}
			}



			if(flag && slots[inputSlotArrayNumber] != null){
				itemstack.stackSize -= itemGroupBasedInputSlotDecrease[getWorkingItemGroupBasedRecipe(slots)][inputSlotArrayNumber];
				if(itemstack.stackSize <= 0){
					return null;
				}
			}
		}
	}
	return itemstack;	
}

Some code that handles NBT Crafting

if(itemGroupBasedRecipeInput[l][m - outPutSlots] != null){
						for(int v = 0; v < itemGroupBasedRecipeInput[l][m - outPutSlots].getItemLength(); v++){
							itemGroupBasedfinalItemStacks[l][m][v] = new ItemStack(Items.diamond_horse_armor);
							System.out.println("\t\t\t\t\t ----------");
							System.out.println(itemGroupBasedfinalItemStacks[l][m][v] + "\t" + l + "\t" + m + "\t" + v);
							itemGroupBasedfinalItemStacks[l][m][v].stackSize = itemGroupBasedRecipeOutputStackSize[l][m];
							if(itemGroupBasedNBTagFlag[l][m] == true && itemGroupBasedRecipeInput[l][m - outPutSlots] != null){
								itemGroupBasedfinalItemStacks[l][m][v].stackSize = 1;
								itemGroupBasedfinalItemStacks[l][m][v].stackTagCompound = new NBTTagCompound();
								for(int n = 0; n < itemGroupBasedMaxNBTTagStringsOnSlot; n++){
									try{
										itemGroupBasedfinalItemStacks[l][m][v].stackTagCompound.setString(n+"", itemGroupBasedOutputNBTString[l][slots.length - 1 - m][n]);
									}catch(Exception e){
									}
								}
							}
						}

The Tile Entity update Code

this.slots[0] = rh.addInputSlotManager(slots, 0);
	this.slots[1] = rh.addInputSlotManager(slots, 1);
	if(slots[2] == null && rh.getWorkingItemGroupBasedRecipe(slots) != -1 && System.currentTimeMillis() -10 > lastCrafted && !(System.currentTimeMillis()-50 > lastCrafted)){
		System.out.println("Gecraftet");
	}

	this.slots[2] = rh.addOutputSlotManagerforItemBase(slots, 2);
	if(rh.getWorkingItemGroupBasedRecipe(slots) != -1){
		lastCrafted = System.currentTimeMillis();
	}

Ignore those Yolos They are just for me, to look when it does this