The transformation into Docbook 5.0 files is performed by means of a script. Even though it has been tested on several Docbook 4.x files, it's not infallible.
You are advised to keep the 'Validate after transformation' option to ensure the transformed document is compliant with Docbook 5.0
If the transformed document is not compliant with Docbook 5.0, you will receive a notice and the transformed document on which you need to perform manual modifications.