Managed to get this working.
For future reference:
First we need to edit the custom post type to allow parent-child relationship (set “Hierarchical” option to true)
Then we can add an advanced custom fields group to the parent page:
Show this field group if -> post type is equal to [custom post type] AND
page type is equal to Top level page
And a seperate advanced custom fields group for the children pages:
Show this field group if -> post type is equal to [custom post type] AND
page type is equal to Child page
BTW, no edit option for posts here?