diff --git a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
index ac033f7db60..13712cee01d 100644
--- a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
+++ b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
@@ -471,6 +471,7 @@ class PaymentReconciliation(Document):
 
 	def build_qb_filter_conditions(self, get_invoices=False, get_return_invoices=False):
 		self.common_filter_conditions.clear()
+		self.accounting_dimension_filter_conditions.clear()
 		self.ple_posting_date_filter.clear()
 		ple = qb.DocType("Payment Ledger Entry")
 
diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index 7ba433ea8c8..31885ac07b3 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -439,8 +439,7 @@ def reconcile_against_document(args):  # nosemgrep
 		# cancel advance entry
 		doc = frappe.get_doc(voucher_type, voucher_no)
 		frappe.flags.ignore_party_validation = True
-		gl_map = doc.build_gl_map()
-		create_payment_ledger_entry(gl_map, cancel=1, adv_adj=1)
+		_delete_pl_entries(voucher_type, voucher_no)
 
 		for entry in entries:
 			check_if_advance_entry_modified(entry)
@@ -452,11 +451,23 @@ def reconcile_against_document(args):  # nosemgrep
 			else:
 				update_reference_in_payment_entry(entry, doc, do_not_save=True)
 
+		if doc.doctype == "Journal Entry":
+			try:
+				doc.validate_total_debit_and_credit()
+			except Exception as validation_exception:
+				raise frappe.ValidationError(_(f"Validation Error for {doc.name}")) from validation_exception
+
 		doc.save(ignore_permissions=True)
 		# re-submit advance entry
 		doc = frappe.get_doc(entry.voucher_type, entry.voucher_no)
 		gl_map = doc.build_gl_map()
-		create_payment_ledger_entry(gl_map, cancel=0, adv_adj=1)
+		create_payment_ledger_entry(gl_map, update_outstanding="No", cancel=0, adv_adj=1)
+
+		# Only update outstanding for newly linked vouchers
+		for entry in entries:
+			update_voucher_outstanding(
+				entry.against_voucher_type, entry.against_voucher, entry.account, entry.party_type, entry.party
+			)
 
 		frappe.flags.ignore_party_validation = False