delete the auto created batch

erpnext/accounts/doctype/purchase_invoice/purchase_invoice.py

@@ -866,7 +866,7 @@ class PurchaseInvoice(BuyingController):
 		# because updating ordered qty in bin depends upon updated ordered qty in PO
 		if self.update_stock == 1:
 			self.update_stock_ledger()
-			self.unlink_reference_from_batch()
+			self.delete_auto_created_batches()
 
 		self.make_gl_entries_on_cancel()
 		self.update_project()

erpnext/controllers/stock_controller.py

@@ -234,12 +234,16 @@ class StockController(AccountsController):
 				frappe.throw(_("{0} {1}: Cost Center is mandatory for Item {2}").format(
 					_(self.doctype), self.name, item.get("item_code")))
 
-	def unlink_reference_from_batch(self):
-		frappe.db.sql(""" UPDATE `tabBatch`
-			SET reference_doctype = NULL, reference_name = NULL
-			WHERE
-				reference_doctype = %s and reference_name = %s
-		""", (self.doctype, self.name))
+	def delete_auto_created_batches(self):
+		for d in self.items:
+			if not d.batch_no: continue
+
+			d.batch_no = None
+			d.db_set("batch_no", None)
+
+		for data in frappe.get_all("Batch",
+			{'reference_name': self.name, 'reference_doctype': self.doctype}):
+			frappe.delete_doc("Batch", data.name)
 
 	def get_sl_entries(self, d, args):
 		sl_dict = frappe._dict({

erpnext/stock/doctype/purchase_receipt/purchase_receipt.py

@@ -195,7 +195,7 @@ class PurchaseReceipt(BuyingController):
 		# because updating ordered qty in bin depends upon updated ordered qty in PO
 		self.update_stock_ledger()
 		self.make_gl_entries_on_cancel()
-		self.unlink_reference_from_batch()
+		self.delete_auto_created_batches()
 
 	def get_current_stock(self):
 		for d in self.get('supplied_items'):

erpnext/stock/doctype/stock_entry/stock_entry.py

@@ -110,7 +110,7 @@ class StockEntry(StockController):
 		self.update_cost_in_project()
 		self.update_transferred_qty()
 		self.update_quality_inspection()
-		self.unlink_reference_from_batch()
+		self.delete_auto_created_batches()
 
 	def set_job_card_data(self):
 		if self.job_card and not self.work_order: