update_user_meta() will update ALL user meta of the same key UNLESS you specify a specific record out of the set that you want to replace.

Here’s a way to do that, specifically for the instance where you have user meta that may look like this:

+---------+----------------------+-----------------
| user_id | meta_key             | meta_value                                                                                               |
+---------+----------------------+-----------------
| 862     | favorite_coffee      | {"coffee_id":10,"title":"Vietnamese Iced Coffee","type":"drip"}                                          
| 862     | favorite_coffee      | {"coffee_id":11,"title":"Mocha","type":"espresso"}                                                       
| 862     | favorite_coffee      | {"coffee_id":12,"title":"Just An Okay Cappuchino","type":"espresso"}

// dummy data to better show the issue, we want to change the title of `coffee_id` 12
$parameters = array(
    'coffee_id' => '12',
    'title' => 'A Delicious Cappuchino',
    'type' => 'espresso',
);

// try to find some `favorite_coffee` user meta 
$previous_favorite_coffee = get_user_meta( $user_id, 'favorite_coffee', false );

/**
* First, the condition for when no favorite_coffee user meta data exists
**/ 
if ( empty( $previous_favorite_coffee ) ) {
    add_user_meta( $user_id, 'favorite_coffee', $parameters );
}

/**
* Second, the condition for when some favorite_coffee user_meta data already exists
**/
// search recursively through records returned from get_user_meta for the record you want to replace, as identified by `coffee_id` - credit: http://php.net/manual/en/function.array-search.php#116635
$coffee_id = array_search( $parameters['coffee_id'], array_column( $previous_favorite_coffee, 'coffee_id' ) );
if ( false === $coffee_id ) {
    // add if the wp_usermeta meta_key[favorite_coffee] => meta_value[ $parameters[ $coffee_id ] ] pair does not exist
    add_user_meta( $user_id, 'favorite_coffee', $parameters );
} else {
    // update if the wp_usermeta meta_key[favorite_coffee] => meta_value[ $parameters[ $coffee_id ] ] pair already exists
    update_user_meta( $user_id, 'favorite_coffee', $parameters, $previous_favorite_coffee[ $coffee_id ] );
}