diff --git a/erpnext/accounts/doctype/payment_request/payment_request.py b/erpnext/accounts/doctype/payment_request/payment_request.py
index ae4cd3f40260710c38e25c8dda635427bd8e85ff..c74da59d3906f2b121d2687c025c24c92aa174eb 100644
--- a/erpnext/accounts/doctype/payment_request/payment_request.py
+++ b/erpnext/accounts/doctype/payment_request/payment_request.py
@@ -606,23 +606,12 @@ class PaymentRequest(Document):
 				self.db_set("status", "Pending", commit=True)
 			self.run_method("set_payment_method_registered")
 
-		self.db_set("transaction_reference", reference_no, commit=True)
+		if not reference_no:
+			self.db_set("transaction_reference", reference_no, commit=True)
 
 		if curr_status in ("Pending", "Paid"):
 			self.register_default_payment_method()
 
-		advance_payment_doctypes = frappe.get_hooks("advance_payment_receivable_doctypes") + frappe.get_hooks(
-			"advance_payment_payable_doctypes"
-		)
-		if self.reference_doctype in advance_payment_doctypes:
-			# set advance payment status
-			self.reload()
-			ref_doc = frappe.get_doc(self.reference_doctype, self.reference_name)
-			ref_doc.set_advance_payment_status(
-				advance_paid=self.grand_total if self.status == "Paid" else 0.0,
-				order_total=ref_doc.get("grand_total"),
-			)
-
 		return self.get_redirection()
 
 	def set_payment_method_registered(self):