diff --git a/frappe/patches.txt b/frappe/patches.txt
index a678367b90..a23f61b899 100644
--- a/frappe/patches.txt
+++ b/frappe/patches.txt
@@ -48,3 +48,4 @@ execute:frappe.db.sql("""update `tabSingles` set `value`=`doctype` where `field`
 frappe.patches.v4_1.enable_print_as_pdf #2014-06-17
 execute:frappe.db.sql("""update `tabDocPerm` set email=1 where parent='User' and permlevel=0 and `role`='All' and `read`=1 and apply_user_permissions=1""") #2014-07-15
 execute:frappe.db.sql("""update `tabPrint Format` set print_format_type='Client' where ifnull(print_format_type, '')=''""") #2014-07-28
+frappe.patches.v4_1.file_manager_fix
diff --git a/frappe/patches/v4_1/file_manager_fix.py b/frappe/patches/v4_1/file_manager_fix.py
new file mode 100644
index 0000000000..c0dd1fecee
--- /dev/null
+++ b/frappe/patches/v4_1/file_manager_fix.py
@@ -0,0 +1,89 @@
+# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
+# MIT License. See license.txt
+
+from __future__ import unicode_literals
+
+import frappe
+import os
+from frappe.utils.file_manager import get_content_hash, get_file, get_file_name
+from frappe.utils import get_files_path, get_site_path
+
+# The files missed by the previous patch might have been replaced with new files
+# with the same filename
+#
+# This patch does the following,
+# * Detect which files were replaced and rename them with name{hash:5}.extn and
+#   update filedata record for the new file
+#
+# * make missing_files.txt in site dir with files that should be recovered from
+#   a backup from a time before version 3 migration
+#
+# * Patch remaining unpatched file data records.
+
+def execute():
+	rename_replacing_files()
+	for name, file_name, file_url in frappe.db.sql(
+			"""select name, file_name, file_url from `tabFile Data`
+			where ifnull(file_name, '')!='' and ifnull(content_hash, '')=''"""):
+		b = frappe.get_doc('File Data', name)
+		old_file_name = b.file_name
+		b.file_name = os.path.basename(old_file_name)
+		if old_file_name.startswith('files/') or old_file_name.startswith('/files/'):
+			b.file_url = os.path.normpath('/' + old_file_name)
+		else:
+			b.file_url = os.path.normpath('/files/' + old_file_name)
+		try:
+			_file_name, content = get_file(name)
+			b.content_hash = get_content_hash(content)
+		except IOError:
+			print 'Warning: Error processing ', name
+			b.content_hash = None
+
+		b.save()
+
+def get_replaced_files():
+	ret = []
+	new_files = dict(frappe.db.sql("select name, file_name from `tabFile Data` where file_name not like 'files/%'"))
+	old_files = dict(frappe.db.sql("select name, file_name from `tabFile Data` where ifnull(content_hash, '')=''"))
+	invfiles = invert_dict(new_files)
+
+	for nname, nfilename in new_files.iteritems():
+		if 'files/' + nfilename in old_files.values():
+			ret.append((nfilename, invfiles[nfilename]))
+	return ret
+
+def rename_replacing_files():
+	replaced_files = get_replaced_files()
+	if len(replaced_files):
+		missing_files = [v[0] for v in replaced_files]
+		with open(get_site_path('missing_files.txt'), 'w') as f:
+			f.write('\n'.join(missing_files) + '\n')
+
+	for file_name, file_datas in replaced_files:
+		print 'processing ' + file_name
+		content_hash = frappe.db.get_value('File Data', file_datas[0], 'content_hash')
+		if not content_hash:
+			continue
+		new_file_name = get_file_name(file_name, content_hash)
+		if os.path.exists(get_files_path(new_file_name)):
+			continue
+			print 'skipping ' + file_name
+		os.rename(get_files_path(file_name), get_files_path(new_file_name))
+		for name in file_datas:
+			f = frappe.get_doc('File Data', name)
+			f.file_name = new_file_name
+			f.file_url = '/files/' + new_file_name
+			f.save()
+
+def invert_dict(ddict):
+	ret = {}
+	for k,v in ddict.iteritems():
+		if not ret.get(v):
+			ret[v] = [k]
+		else:
+			ret[v].append(k)
+	return ret
+
+def get_file_name(fname, hash):
+		partial, extn = fname.rsplit('.', 1)
+		return '{partial}{suffix}.{extn}'.format(partial=partial, extn=extn, suffix=hash[:5])
diff --git a/frappe/utils/file_manager.py b/frappe/utils/file_manager.py
index c78af726de..2e991ba601 100644
--- a/frappe/utils/file_manager.py
+++ b/frappe/utils/file_manager.py
@@ -15,7 +15,7 @@ class MaxFileSizeReachedError(frappe.ValidationError): pass
 
 def get_file_url(file_data_name):
 	data = frappe.db.get_value("File Data", file_data_name, ["file_name", "file_url"], as_dict=True)
-	return data.file_name or data.file_url
+	return data.file_url or data.file_name
 
 def upload():
 	# get record details