diff --git a/erpnext/controllers/accounts_controller.py b/erpnext/controllers/accounts_controller.py
index e3c59d4dab..89f13bbb4b 100644
--- a/erpnext/controllers/accounts_controller.py
+++ b/erpnext/controllers/accounts_controller.py
@@ -346,7 +346,12 @@ class AccountsController(TransactionBase):
 			ple = frappe.qb.DocType("Payment Ledger Entry")
 			frappe.qb.from_(ple).delete().where(
 				(ple.voucher_type == self.doctype) & (ple.voucher_no == self.name)
-				| ((ple.against_voucher_type == self.doctype) & (ple.against_voucher_no == self.name))
+				| (
+					(ple.against_voucher_type == self.doctype)
+					& (ple.against_voucher_no == self.name)
+					& ple.delinked
+					== 1
+				)
 			).run()
 			frappe.db.sql(
 				"delete from `tabGL Entry` where voucher_type=%s and voucher_no=%s", (self.doctype, self.name)