I do, in a way, understand what you are doing. I have a setup where I have a repeater field that lets the client add child posts in the same post type. My setup is different.
On save I have an acf/save_post action that looks at the repeater and compares it with the posts to child posts to see
1) What has been added
2) What has been deleted
and then I add or delete child posts as needed.
In my case I do not have an ID. the child posts are based on start and end date. If any start/end date combination is new I create a new post and for every existing child post if the start/end date combination does not exist then I delete that post.
In my case I store all the needed information in the child posts and not in the repeater.
Have you thought about having a post object field in the child post that points back to the parent instead of a value in the parent that is pointing to the child.
