diff --git a/scripts/upgrade b/scripts/upgrade
index 85f73f9..12ccc5c 100644
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -46,8 +46,22 @@ if [ "$upgrade_type" == "UPGRADE_APP" ]
 then
   ynh_script_progression --message="Upgrading source files..."
 
+  # For aeneria source update, we use a temporary directory because
+  # without it, patches can't be apply correctly:
+  # In 'app-00-ldap-auth.patch' we create a new file, if we try
+  # to apply the patch a second time while the file already exists, it
+  # throws a warning leading to an upgrade fail.
+
+  # Create tmpdir for new sources
+  tmpdir="$(ynh_smart_mktemp min_size=300)"
+
   # Download, check integrity, uncompress and patch the source from app.src
-  ynh_setup_source --dest_dir="$install_dir" --full_replace
+  ynh_setup_source --dest_dir="$tmpdir"
+
+  # Replace the old aeneria by the new one
+  ynh_secure_remove --file="$install_dir"
+  mv "$tmpdir" "$install_dir"
+  ynh_secure_remove --file="$tmpdir"
 fi
 
 chown -R $app:www-data "$install_dir"