Paper/paper-server/nms-patches/Slot.patch

--- a/net/minecraft/server/Slot.java
+++ b/net/minecraft/server/Slot.java
@@ -48,6 +48,9 @@
     }
 
     public boolean hasItem() {
+        if (getItem() != null && getItem().count == 0) {
+            set(null);
+        }
         return this.getItem() != null;
     }