I am struggling with ACF as well when showing certain fields based on the post category/taxonomy selected.
I’m guessing ACF is specifically comparing with the checkbox’s “name” or “type” attribute for the taxonomies and categories. Since the new radio buttons differ it’s causing an issue, at least that’s what I am guessing.
@helgatheviking My suggestion, maybe not best, could you perhaps update the checkbox values based on the correlating radio selections? Depending on what your code does keeping the checkboxes there but hidden?
I think async with JS or on save with PHP could work. I have very limited experience with plugin development though so I am sure it’s not that easy.