diff --git a/erpnext/stock/stock_ledger.py b/erpnext/stock/stock_ledger.py
index 0eafe4323a2..fb8e63c37b7 100644
--- a/erpnext/stock/stock_ledger.py
+++ b/erpnext/stock/stock_ledger.py
@@ -895,7 +895,7 @@ class update_entries_after:
 			# Only run in reposting
 			self.get_serialized_values(sle)
 			self.wh_data.qty_after_transaction += flt(sle.actual_qty)
-			if sle.voucher_type == "Stock Reconciliation" and not sle.batch_no:
+			if sle.voucher_type == "Stock Reconciliation" and not sle.batch_no and has_correct_data(sle):
 				self.wh_data.qty_after_transaction = sle.qty_after_transaction
 
 			self.wh_data.stock_value = flt(self.wh_data.qty_after_transaction) * flt(
@@ -2470,3 +2470,28 @@ def get_incoming_rate_for_serial_and_batch(item_code, row, sn_obj, company):
 @frappe.request_cache
 def is_repack_entry(stock_entry_id):
 	return frappe.get_cached_value("Stock Entry", stock_entry_id, "purpose") == "Repack"
+
+
+def has_correct_data(sle):
+	previous_sle = get_previous_sle(
+		{
+			"item_code": sle.item_code,
+			"warehouse": sle.warehouse,
+			"posting_date": sle.posting_date,
+			"posting_time": sle.posting_time,
+			"creation": sle.creation,
+			"sle": sle.name,
+		}
+	)
+
+	if not previous_sle:
+		return True
+
+	previous_qty = previous_sle.get("qty_after_transaction") or 0
+	if previous_qty and not frappe.db.get_value(
+		"Stock Ledger Entry",
+		{"voucher_detail_no": sle.voucher_detail_no, "is_cancelled": 0, "actual_qty": ("<", 0)},
+	):
+		return False
+
+	return True