I have an HTML file that needs transparency, so I'm using the PDF/X-4 profile (with the command line option --pdf-profile).

However, this removes all links. When I switch back to use PDF/A-1a the links convert fine.

Is this a bug or by design? If the latter, what can I do to get the links back?

Thank you!

This is by design. PDF/X-4 doesn't allow links (or nearly any other annotations).

Thank you @wangp. I'll implement a workaround.