diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index e5678a62105..58c65aeaa52 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -1318,6 +1318,7 @@ class PaymentEntry(AccountsController):
 
 			if self.book_advance_payments_in_separate_party_account:
 				if d.reference_doctype in advance_payment_doctypes:
+					# Upon reconciliation, whole ledger will be reposted. So, reference to SO/PO is fine
 					gle.update(
 						{
 							"against_voucher_type": d.reference_doctype,
@@ -1325,6 +1326,7 @@ class PaymentEntry(AccountsController):
 						}
 					)
 				else:
+					# Do not reference Invoices while Advance is in separate party account
 					gle.update({"against_voucher_type": self.doctype, "against_voucher": self.name})
 			else:
 				gle.update(
diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index 671e46c559c..c7de27c2700 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -486,8 +486,8 @@ def reconcile_against_document(
 		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
+		# When Advance is allocated from an Order to an Invoice
+		# whole ledger must be reposted
 		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:
@@ -527,11 +527,13 @@ def reconcile_against_document(
 		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` in separate account feature
-			# TODO: find a more efficient way post only for the new linked vouchers
+			# When Advance is allocated from an Order to an Invoice
+			# whole ledger must be reposted
 			if repost_whole_ledger:
 				doc.make_gl_entries()
 			else:
+				# 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
 				doc.make_advance_gl_entries()
 		else:
 			gl_map = doc.build_gl_map()