All custom fields (including those created by ACF) are stored as custom post metas of the associated page/post or custom post type.
Page variants in Nelio A/B Testing are exactly the same as regular WordPress pages—Nelio A/B Testing simply adds a meta property in those pages and labels them as being “alternative content in a page test.” The same applies to posts and custom post types.
When our plugin creates a variant of a tested page/post or custom post type, it also duplicates all the fields in the variant. When the user edits a variant of a tested page, they’ll find an exact copy of the tested page first, which they can then tweak and adapt as they please.
If you’re using Advanced Custom Fields, things should work out of the box, as any fields that apply to a page (or a post) will also be visible in an alternative page (or post). However, some users create field groups in a way such that show up only on specific templates, categories and more. Make sure the ACF fields you’re missing do not have this limitation and, if they do, add the template or category the to the variant so that it matches the group field location rule.