diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index e2632d3..0dea1eb 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -473,6 +473,8 @@
 		doc = frappe.get_doc(voucher_type, voucher_no)
 		frappe.flags.ignore_party_validation = True
 
+		# For payments with `Advance` in separate account feature enabled, only new ledger entries are posted for each reference.
+		# No need to cancel/delete payment ledger entries
 		if not (voucher_type == "Payment Entry" and doc.book_advance_payments_in_separate_party_account):
 			_delete_pl_entries(voucher_type, voucher_no)
 
@@ -489,7 +491,7 @@
 				entry.update({"referenced_row": referenced_row})
 				doc.make_exchange_gain_loss_journal([entry])
 			else:
-				update_reference_in_payment_entry(
+				referenced_row = update_reference_in_payment_entry(
 					entry, doc, do_not_save=True, skip_ref_details_update_for_pe=skip_ref_details_update_for_pe
 				)
 
@@ -498,8 +500,8 @@
 		doc = frappe.get_doc(entry.voucher_type, entry.voucher_no)
 
 		if voucher_type == "Payment Entry" and doc.book_advance_payments_in_separate_party_account:
-			# both ledgers must be posted to for `Advance as Liability`
-			doc.make_advance_gl_entries()
+			# both ledgers must be posted to for `Advance` in separate account feature
+			doc.make_advance_gl_entries(referenced_row, update_outstanding="No")
 		else:
 			gl_map = doc.build_gl_map()
 			create_payment_ledger_entry(gl_map, update_outstanding="No", cancel=0, adv_adj=1)
@@ -681,11 +683,12 @@
 			new_row.docstatus = 1
 			for field in list(reference_details):
 				new_row.set(field, reference_details[field])
-
+			row = new_row
 	else:
 		new_row = payment_entry.append("references")
 		new_row.docstatus = 1
 		new_row.update(reference_details)
+		row = new_row
 
 	payment_entry.flags.ignore_validate_update_after_submit = True
 	payment_entry.clear_unallocated_reference_document_rows()
@@ -700,6 +703,7 @@
 
 	if not do_not_save:
 		payment_entry.save(ignore_permissions=True)
+	return row
 
 
 def cancel_exchange_gain_loss_journal(
@@ -876,7 +880,13 @@
 			try:
 				pe_doc = frappe.get_doc("Payment Entry", pe)
 				pe_doc.set_amounts()
-				pe_doc.make_advance_gl_entries(against_voucher_type=ref_type, against_voucher=ref_no, cancel=1)
+
+				# Call cancel on only removed reference
+				references = [
+					x for x in pe_doc.references if x.reference_doctype == ref_type and x.reference_name == ref_no
+				]
+				[pe_doc.make_advance_gl_entries(x, cancel=1) for x in references]
+
 				pe_doc.clear_unallocated_reference_document_rows()
 				pe_doc.validate_payment_type_with_outstanding()
 			except Exception as e: