The difference between a refresh and a shallow index is that a refresh is handled entirely within Digital Hive. It updates local information such as the name of an object, tags, custom fields, and ratings so the UI reflects the latest metadata. This operation does not inspect underlying content changes.
A shallow index goes further. It checks the underlying content system for that specific level or folder to detect changes such as newly added reports or folders that were not present during the last index. This allows Digital Hive to update the index for just that area without having to reindex the entire system.