You may use the acfcdt/custom_table_value_updated
action hook to run custom functionality after a field value has been
saved in a custom database table.
A common use case could be to delete core meta table values as they are saved in a custom table. e.g;
add_action( 'acfcdt/custom_table_value_updated', function ( $value, $post_id, $field_array ) {
// Delete the value entry from the core meta table.
delete_post_meta( $post_id, $field_array['name']);
// Delete the key reference from the core meta table. Note: this can break ACF's ability to locate the field array
// and create problems later on if no field references are available through other means. Only do this if you have
// ACF JSON enabled.
delete_post_meta( $post_id, "_{$field_array['name']}")
}, 10, 3 );