How do I update a specific object in an array, in user meta?

You can just assign a new value to the 1h_userbadge_comments25 key.

Like so…

<?php
$meta_value = get_user_meta($user_id, 'lh_userbadges', false);
// just assign this key a new value
$meta_value['lh_userbadge_comments25'] = 25;

Then just save it again.

<?php
update_user_meta( $user_id, 'lh_userbadges', $meta_value );

Whether or not storing all of those values as an array is the correct way to do this is really up to you. Do you need to do a lot of changing around like this? Do the all these values make sense together? Without knowing more about what you’re doing, that’s a hard question to answer.