Notify the parent container of a lot more thoroughly when the slot is changed (i.e. items taken from it).

And then make use of that to invalidate the validation state of the crafting pattern in the Molecular Assembler when the pattern is changed.

src/main/java/appeng/container/implementations/ContainerMolecularAssembler.java

@@ -21,6 +21,7 @@ package appeng.container.implementations;
 import net.minecraft.entity.player.PlayerEntity;
 import net.minecraft.entity.player.PlayerInventory;
 import net.minecraft.inventory.container.ContainerType;
+import net.minecraft.inventory.container.Slot;
 import net.minecraft.item.ItemStack;
 import net.minecraft.network.PacketBuffer;
 import net.minecraft.world.World;
@@ -33,6 +34,7 @@ import appeng.api.networking.crafting.ICraftingPatternDetails;
 import appeng.container.ContainerLocator;
 import appeng.container.guisync.GuiSync;
 import appeng.container.interfaces.IProgressProvider;
+import appeng.container.slot.AppEngSlot;
 import appeng.container.slot.SlotMolecularAssemblerPattern;
 import appeng.container.slot.SlotOutput;
 import appeng.container.slot.SlotRestrictedInput;
@@ -60,6 +62,8 @@ public class ContainerMolecularAssembler extends ContainerUpgradeable implements
     @GuiSync(4)
     public int craftProgress = 0;
 
+    private Slot encodedPatternSlot;
+
     public ContainerMolecularAssembler(int id, final PlayerInventory ip, final TileMolecularAssembler te) {
         super(TYPE, id, ip, te);
         this.tma = te;
@@ -108,8 +112,9 @@ public class ContainerMolecularAssembler extends ContainerUpgradeable implements
         offX = 126;
         offY = 16;
 
-        this.addSlot(new SlotRestrictedInput(SlotRestrictedInput.PlacableItemType.ENCODED_CRAFTING_PATTERN, mac, 10,
-                offX, offY, this.getPlayerInventory()));
+        encodedPatternSlot = this
+                .addSlot(new SlotRestrictedInput(SlotRestrictedInput.PlacableItemType.ENCODED_CRAFTING_PATTERN, mac, 10,
+                        offX, offY, this.getPlayerInventory()));
         this.addSlot(new SlotOutput(mac, 9, offX, offY + 32, -1));
 
         offX = 122;
@@ -161,4 +166,19 @@ public class ContainerMolecularAssembler extends ContainerUpgradeable implements
     public int getMaxProgress() {
         return MAX_CRAFT_PROGRESS;
     }
+
+    @Override
+    public void onSlotChange(Slot s) {
+
+        // If the pattern changes, the crafting grid slots lose validity
+        if (s == encodedPatternSlot) {
+            for (Slot otherSlot : inventorySlots) {
+                if (otherSlot != s && otherSlot instanceof AppEngSlot) {
+                    ((AppEngSlot) otherSlot).setIsValid(AppEngSlot.CalculatedValidity.NotAvailable);
+                }
+            }
+        }
+
+    }
+
 }