This question sounds like it’s related directly to this other question http://support.advancedcustomfields.com/forums/topic/wp-loop-via-checkbox-value/
The pagination function will work without doing a new query for your custom post type. I wouldn’t follow that post.
The correct way to do this is to create a template for your custom post type archive following the WP template hierarchy and then do a pre_get_posts action like I showed in that question.
Previous and next post link function are documented here https://codex.wordpress.org/Function_Reference/previous_posts_link and here https://codex.wordpress.org/Template_Tags/next_posts_link
