diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index 1a89c45..7970a3e 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -1299,7 +1299,7 @@
 		if getdate(posting_date) < getdate(self.posting_date):
 			posting_date = self.posting_date
 
-		dr_or_cr = "credit" if invoice.reference_doctype == "Sales Invoice" else "debit"
+		dr_or_cr = "credit" if invoice.reference_doctype in ["Sales Invoice", "Sales Order"] else "debit"
 		args_dict["account"] = invoice.account
 		args_dict[dr_or_cr] = invoice.allocated_amount
 		args_dict[dr_or_cr + "_in_account_currency"] = invoice.allocated_amount
diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index b436d02..0755f2e 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -490,7 +490,9 @@
 
 		# 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):
+		if voucher_type == "Payment Entry" and doc.book_advance_payments_in_separate_party_account:
+			doc.make_advance_gl_entries(cancel=1)
+		else:
 			_delete_pl_entries(voucher_type, voucher_no)
 
 		for entry in entries:
@@ -501,14 +503,16 @@
 
 			# update ref in advance entry
 			if voucher_type == "Journal Entry":
-				referenced_row = update_reference_in_journal_entry(entry, doc, do_not_save=False)
+				referenced_row, update_advance_paid = update_reference_in_journal_entry(
+					entry, doc, do_not_save=False
+				)
 				# advance section in sales/purchase invoice and reconciliation tool,both pass on exchange gain/loss
 				# amount and account in args
 				# referenced_row is used to deduplicate gain/loss journal
 				entry.update({"referenced_row": referenced_row})
 				doc.make_exchange_gain_loss_journal([entry], dimensions_dict)
 			else:
-				referenced_row = update_reference_in_payment_entry(
+				referenced_row, update_advance_paid = update_reference_in_payment_entry(
 					entry,
 					doc,
 					do_not_save=True,
@@ -522,7 +526,7 @@
 
 		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
-			doc.make_advance_gl_entries(cancel=1)
+			# 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()
@@ -533,6 +537,10 @@
 			update_voucher_outstanding(
 				entry.against_voucher_type, entry.against_voucher, entry.account, entry.party_type, entry.party
 			)
+		# update advance paid in Advance Receivable/Payable doctypes
+		if update_advance_paid:
+			for t, n in update_advance_paid:
+				frappe.get_doc(t, n).set_total_advance_paid()
 
 		frappe.flags.ignore_party_validation = False
 
@@ -622,11 +630,12 @@
 	jv_detail = journal_entry.get("accounts", {"name": d["voucher_detail_no"]})[0]
 
 	# Update Advance Paid in SO/PO since they might be getting unlinked
+	update_advance_paid = []
 	advance_payment_doctypes = frappe.get_hooks(
 		"advance_payment_receivable_doctypes"
 	) + frappe.get_hooks("advance_payment_payable_doctypes")
 	if jv_detail.get("reference_type") in advance_payment_doctypes:
-		frappe.get_doc(jv_detail.reference_type, jv_detail.reference_name).set_total_advance_paid()
+		update_advance_paid.append((jv_detail.reference_type, jv_detail.reference_name))
 
 	if flt(d["unadjusted_amount"]) - flt(d["allocated_amount"]) != 0:
 		# adjust the unreconciled balance
@@ -675,7 +684,7 @@
 	if not do_not_save:
 		journal_entry.save(ignore_permissions=True)
 
-	return new_row.name
+	return new_row.name, update_advance_paid
 
 
 def update_reference_in_payment_entry(
@@ -694,6 +703,7 @@
 		"account": d.account,
 		"dimensions": d.dimensions,
 	}
+	update_advance_paid = []
 
 	if d.voucher_detail_no:
 		existing_row = payment_entry.get("references", {"name": d["voucher_detail_no"]})[0]
@@ -703,9 +713,7 @@
 			"advance_payment_receivable_doctypes"
 		) + frappe.get_hooks("advance_payment_payable_doctypes")
 		if existing_row.get("reference_doctype") in advance_payment_doctypes:
-			frappe.get_doc(
-				existing_row.reference_doctype, existing_row.reference_name
-			).set_total_advance_paid()
+			update_advance_paid.append((existing_row.reference_doctype, existing_row.reference_name))
 
 		if d.allocated_amount <= existing_row.allocated_amount:
 			existing_row.allocated_amount -= d.allocated_amount
@@ -735,7 +743,7 @@
 
 	if not do_not_save:
 		payment_entry.save(ignore_permissions=True)
-	return row
+	return row, update_advance_paid
 
 
 def cancel_exchange_gain_loss_journal(
diff --git a/erpnext/controllers/accounts_controller.py b/erpnext/controllers/accounts_controller.py
index a3db196..aa3d3e0 100644
--- a/erpnext/controllers/accounts_controller.py
+++ b/erpnext/controllers/accounts_controller.py
@@ -1864,7 +1864,7 @@
 				(ple.against_voucher_type == self.doctype)
 				& (ple.against_voucher_no == self.name)
 				& (ple.party == party)
-				& (ple.docstatus == 1)
+				& (ple.delinked == 0)
 				& (ple.company == self.company)
 			)
 			.run(as_dict=True)