diff --git a/VERSION b/VERSION
index b01b5d99..43ff51c1 100755
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-4.0.9-develop2
+4.0.9-develop3
diff --git a/modules/config.py b/modules/config.py
index b7b0b29f..30021a24 100755
--- a/modules/config.py
+++ b/modules/config.py
@@ -688,7 +688,8 @@ def cleanup_dirs(self, location):
                     if num_del > 0:
                         if not self.dry_run:
                             for path in location_path_list:
-                                util.remove_empty_directories(path, "**/*")
+                                if path != location_path:
+                                    util.remove_empty_directories(path, "**/*")
                         body += logger.print_line(
                             f"{'Did not delete' if self.dry_run else 'Deleted'} {num_del} files "
                             f"({util.human_readable_size(size_bytes)}) from the {location}.",