Turns out it was this piece of code in functions.php that we were using to re-write the slugs on save of the posts was the issue:
function myplugin_update_slug( $data, $postarr ) {
if ( ! in_array( $data[‘post_status’], array( ‘draft’, ‘pending’, ‘auto-draft’ ) ) ) {
$data[‘post_name’] = sanitize_title( $data[‘post_title’] );
}
return $data;
}
The sanitize_title() function was overwriting the key field and causing ACF to lose track of the fields.
We resolved this by activating a clean WP theme, then once we confirmed that it was some code in our child theme we just commented out code in our functions.php file until the offending function was found.
