What you describe are the usual media bay messages, when registered content is missing.
I already tested it by myself: H6 content can be completely stripped down - if you don’t need factory content. Of course you can’t play patches with missing samples. But you even may play wavetable patches, because they don’t rely on sample content, as the wavetable data is stored within every patch.
The library manager allows to uninstall selected content afterwards, so consequently there should be an option to only download selected content beforehand.