You need to use the update_field() function. http://www.advancedcustomfields.com/resources/update_field/
There are details on updating a repeater. It is for a taxonomy, but it will work on a post as well, just use the posts ID.
YOu will need to do this in a pre save post filter, this is explained here http://www.advancedcustomfields.com/resources/acf-pre_save_post/
