There is a filter, it can be used in some cases but the results can be broken in other cases. The only thing you can do is try it and see if it works.
http://www.advancedcustomfields.com/resources/acf-fields-relationship-query/
I know that if the relationship is for a hierarchical post type, changing the orderby value breaks the results because ACF groups them by parent. There may be other issues that I’m not aware of as well.
