I'm not familiar with the legislation so took a look. I couldn't see anything specific in it so I'd go with general traceability, due diligence and common sense. If you would rely on that paperwork in an incident, to a customer or in court to prove the traceability or that the batch was safe, the right quality etc, I would want the lot number on it.
So for example, if you have a certificate of conformance, it's not necessarily related to the batch but to the controls in general so I wouldn't demand a lot code on that. If you wanted a delivery note to be proof of when that batch arrived on site, I would want a lot code on it. If you want a certificate of analysis which is specifically related to that batch (e.g. reducing sugar content of potatoes from a specific store), then I'd want the lot code on it.