diff --git a/erpnext/accounts/doctype/sales_invoice/sales_invoice.py b/erpnext/accounts/doctype/sales_invoice/sales_invoice.py
index 9077ee73b3af..8927ce3d6ac8 100644
--- a/erpnext/accounts/doctype/sales_invoice/sales_invoice.py
+++ b/erpnext/accounts/doctype/sales_invoice/sales_invoice.py
@@ -1260,14 +1260,14 @@ def make_gle_for_rounding_adjustment(self, gl_entries):
 	def update_billing_status_in_dn(self, update_modified=True):
 		updated_delivery_notes = []
 		for d in self.get("items"):
-			if d.dn_detail:
+			if d.so_detail:
+				updated_delivery_notes += update_billed_amount_based_on_so(d.so_detail, update_modified)
+			elif d.dn_detail:
 				billed_amt = frappe.db.sql("""select sum(amount) from `tabSales Invoice Item`
 					where dn_detail=%s and docstatus=1""", d.dn_detail)
 				billed_amt = billed_amt and billed_amt[0][0] or 0
 				frappe.db.set_value("Delivery Note Item", d.dn_detail, "billed_amt", billed_amt, update_modified=update_modified)
 				updated_delivery_notes.append(d.delivery_note)
-			elif d.so_detail:
-				updated_delivery_notes += update_billed_amount_based_on_so(d.so_detail, update_modified)
 
 		for dn in set(updated_delivery_notes):
 			frappe.get_doc("Delivery Note", dn).update_billing_percentage(update_modified=update_modified)
diff --git a/erpnext/patches.txt b/erpnext/patches.txt
index bcc0c019bf1f..569fd96e8a3a 100644
--- a/erpnext/patches.txt
+++ b/erpnext/patches.txt
@@ -345,4 +345,4 @@ erpnext.patches.v13_0.agriculture_deprecation_warning
 erpnext.patches.v13_0.update_maintenance_schedule_field_in_visit
 erpnext.patches.v13_0.hospitality_deprecation_warning
 erpnext.patches.v13_0.delete_bank_reconciliation_detail
-erpnext.patches.v13_0.update_sane_transfer_against
+erpnext.patches.v13_0.update_sane_transfer_against
\ No newline at end of file
diff --git a/erpnext/stock/doctype/delivery_note/delivery_note.py b/erpnext/stock/doctype/delivery_note/delivery_note.py
index d1e22440b962..c3247fbe3e82 100644
--- a/erpnext/stock/doctype/delivery_note/delivery_note.py
+++ b/erpnext/stock/doctype/delivery_note/delivery_note.py
@@ -339,17 +339,35 @@ def make_return_invoice(self):
 			frappe.throw(_("Could not create Credit Note automatically, please uncheck 'Issue Credit Note' and submit again"))
 
 def update_billed_amount_based_on_so(so_detail, update_modified=True):
+	from frappe.query_builder.functions import Sum
+
 	# Billed against Sales Order directly
-	billed_against_so = frappe.db.sql("""select sum(amount) from `tabSales Invoice Item`
-		where so_detail=%s and (dn_detail is null or dn_detail = '') and docstatus=1""", so_detail)
+	si = frappe.qb.DocType("Sales Invoice").as_("si")
+	si_item = frappe.qb.DocType("Sales Invoice Item").as_("si_item")
+	sum_amount = Sum(si_item.amount).as_("amount")
+
+	billed_against_so = frappe.qb.from_(si).from_(si_item).select(sum_amount).where(
+		(si_item.parent == si.name) &
+		(si_item.so_detail == so_detail) &
+		((si_item.dn_detail.isnull()) | (si_item.dn_detail == '')) &
+		(si_item.docstatus == 1) &
+		(si.update_stock == 0)
+	).run()
 	billed_against_so = billed_against_so and billed_against_so[0][0] or 0
 
 	# Get all Delivery Note Item rows against the Sales Order Item row
-	dn_details = frappe.db.sql("""select dn_item.name, dn_item.amount, dn_item.si_detail, dn_item.parent
-		from `tabDelivery Note Item` dn_item, `tabDelivery Note` dn
-		where dn.name=dn_item.parent and dn_item.so_detail=%s
-			and dn.docstatus=1 and dn.is_return = 0
-		order by dn.posting_date asc, dn.posting_time asc, dn.name asc""", so_detail, as_dict=1)
+
+	dn = frappe.qb.DocType("Delivery Note").as_("dn")
+	dn_item = frappe.qb.DocType("Delivery Note Item").as_("dn_item")
+
+	dn_details = frappe.qb.from_(dn).from_(dn_item).select(dn_item.name, dn_item.amount, dn_item.si_detail, dn_item.parent, dn_item.stock_qty, dn_item.returned_qty).where(
+		(dn.name == dn_item.parent) &
+		(dn_item.so_detail == so_detail) &
+		(dn.docstatus == 1) &
+		(dn.is_return == 0)
+	).orderby(
+		dn.posting_date, dn.posting_time, dn.name
+	).run(as_dict=True)
 
 	updated_dn = []
 	for dnd in dn_details:
@@ -367,7 +385,11 @@ def update_billed_amount_based_on_so(so_detail, update_modified=True):
 
 		# Distribute billed amount directly against SO between DNs based on FIFO
 		if billed_against_so and billed_amt_agianst_dn < dnd.amount:
-			pending_to_bill = flt(dnd.amount) - billed_amt_agianst_dn
+			if dnd.returned_qty:
+				pending_to_bill = flt(dnd.amount) * (dnd.stock_qty - dnd.returned_qty) / dnd.stock_qty
+			else:
+				pending_to_bill = flt(dnd.amount)
+			pending_to_bill -= billed_amt_agianst_dn
 			if pending_to_bill <= billed_against_so:
 				billed_amt_agianst_dn += pending_to_bill
 				billed_against_so -= pending_to_bill