Html5 - multiple elements with H1

Have I got this wrong?

The new elements that html5 brought allowed us to use headers within sections, nav etc. Does this apply to H1? And if it is allowed - does it make bad SEO sense?

The reason I ask is that most, if not all, the SEO ranking tools out there, tell me to remove duplicate H1's from my code. It's a good few years since the introduction of these new elements so I would have though the major tools would be up to date with the structure.

Any advice appreciated.