Because the way that you are including the fields the are being considered top level fields and not sub fields a layout. The values are likely being stored in the DB under the name of the sub field. Each subsequent submission will overwrite the last values.
The only way that I can think of doing this is to create an acf/save_post filter https://www.advancedcustomfields.com/resources/acf-save_post/ and in this filter you would need to update the flex field/layout/sub fields based on the current values of these other fields that are stored incorrectly. I’m not sure how you’d do this.
