fix: don't update reference to SI / PI on advances

erpnext/accounts/doctype/payment_entry/payment_entry.py

@@ -1308,11 +1308,23 @@ class PaymentEntry(AccountsController):
 				{
 					dr_or_cr: allocated_amount_in_company_currency,
 					dr_or_cr + "_in_account_currency": d.allocated_amount,
-					"against_voucher_type": d.reference_doctype,
-					"against_voucher": d.reference_name,
 					"cost_center": cost_center,
 				}
 			)
+
+			if self.book_advance_payments_in_separate_party_account and d.reference_doctype in [
+				"Sales Order",
+				"Purchase Order",
+			]:
+				gle.update(
+					{
+						"against_voucher_type": d.reference_doctype,
+						"against_voucher": d.reference_name,
+					}
+				)
+			else:
+				gle.update({"against_voucher_type": self.doctype, "against_voucher": self.name})
+
 			gl_entries.append(gle)
 
 		if self.unallocated_amount:

erpnext/accounts/utils.py

@@ -488,7 +488,11 @@ def reconcile_against_document(
 
 		# 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
+		repost_whole_ledger = any([x.voucher_detail_no for x in entries])
 		if voucher_type == "Payment Entry" and doc.book_advance_payments_in_separate_party_account:
+			if repost_whole_ledger:
+				doc.make_gl_entries(cancel=1)
+			else:
 				doc.make_advance_gl_entries(cancel=1)
 		else:
 			_delete_pl_entries(voucher_type, voucher_no)
@@ -525,6 +529,9 @@ def reconcile_against_document(
 		if voucher_type == "Payment Entry" and doc.book_advance_payments_in_separate_party_account:
 			# both ledgers must be posted to for `Advance` in separate account feature
 			# TODO: find a more efficient way post only for the new linked vouchers
+			if repost_whole_ledger:
+				doc.make_gl_entries()
+			else:
 				doc.make_advance_gl_entries()
 		else:
 			gl_map = doc.build_gl_map()