diff --git a/erpnext/accounts/doctype/bank_transaction/bank_transaction.py b/erpnext/accounts/doctype/bank_transaction/bank_transaction.py
index 0544a46..7ea71fc 100644
--- a/erpnext/accounts/doctype/bank_transaction/bank_transaction.py
+++ b/erpnext/accounts/doctype/bank_transaction/bank_transaction.py
@@ -55,6 +55,11 @@
 				self.clear_sales_invoice(payment_entry, for_cancel=for_cancel)
 
 	def clear_simple_entry(self, payment_entry, for_cancel=False):
+		if payment_entry.payment_document == "Payment Entry":
+			if frappe.db.get_value("Payment Entry", payment_entry.payment_entry, "payment_type") == "Internal Transfer":
+				if len(get_reconciled_bank_transactions(payment_entry)) < 2:
+					return
+
 		clearance_date = self.date if not for_cancel else None
 		frappe.db.set_value(
 			payment_entry.payment_document, payment_entry.payment_entry,
@@ -70,6 +75,17 @@
 			),
 			"clearance_date", clearance_date)
 
+def get_reconciled_bank_transactions(payment_entry):
+	reconciled_bank_transactions = frappe.get_all(
+		'Bank Transaction Payments', 
+		filters = {
+			'payment_entry': payment_entry.payment_entry
+		},
+		fields = ['parent']
+	)
+
+	return reconciled_bank_transactions
+
 def get_total_allocated_amount(payment_entry):
 	return frappe.db.sql("""
 		SELECT
diff --git a/erpnext/patches.txt b/erpnext/patches.txt
index bf0446b..0a6a8bd 100644
--- a/erpnext/patches.txt
+++ b/erpnext/patches.txt
@@ -295,5 +295,6 @@
 erpnext.patches.v13_0.add_custom_field_for_south_africa #2
 erpnext.patches.v13_0.update_recipient_email_digest
 erpnext.patches.v13_0.shopify_deprecation_warning
+erpnext.patches.v13_0.reset_clearance_date_for_intracompany_payment_entries
 erpnext.patches.v13_0.einvoicing_deprecation_warning
 erpnext.patches.v14_0.delete_einvoicing_doctypes
diff --git a/erpnext/patches/v13_0/reset_clearance_date_for_intracompany_payment_entries.py b/erpnext/patches/v13_0/reset_clearance_date_for_intracompany_payment_entries.py
new file mode 100644
index 0000000..1da5275
--- /dev/null
+++ b/erpnext/patches/v13_0/reset_clearance_date_for_intracompany_payment_entries.py
@@ -0,0 +1,45 @@
+# Copyright (c) 2019, Frappe and Contributors
+# License: GNU General Public License v3. See license.txt
+
+from __future__ import unicode_literals
+
+import frappe
+
+def execute():
+    """
+        Reset Clearance Date for Payment Entries of type Internal Transfer that have only been reconciled with one Bank Transaction.
+        This will allow the Payment Entries to be reconciled with the second Bank Transaction using the Bank Reconciliation Tool.
+    """
+
+    intra_company_pe = get_intra_company_payment_entries_with_clearance_dates()
+    reconciled_bank_transactions = get_reconciled_bank_transactions(intra_company_pe)
+
+    for payment_entry in reconciled_bank_transactions:
+        if len(reconciled_bank_transactions[payment_entry]) == 1:
+            frappe.db.set_value('Payment Entry', payment_entry, 'clearance_date', None)
+
+def get_intra_company_payment_entries_with_clearance_dates():
+    return frappe.get_all(
+        'Payment Entry',
+        filters = {
+            'payment_type': 'Internal Transfer',
+            'clearance_date': ["not in", None]
+        },
+        pluck = 'name'
+    )
+
+def get_reconciled_bank_transactions(intra_company_pe):
+    """Returns dictionary where each key:value pair is Payment Entry : List of Bank Transactions reconciled with Payment Entry"""
+
+    reconciled_bank_transactions = {}
+
+    for payment_entry in intra_company_pe:
+        reconciled_bank_transactions[payment_entry] = frappe.get_all(
+            'Bank Transaction Payments', 
+            filters = {
+                'payment_entry': payment_entry
+            }, 
+            pluck='parent'
+        )
+
+    return reconciled_bank_transactions
\ No newline at end of file