Manually changing URL alias values via phpmyadmin? What does this affect?
Doing any manual updates to the Drupal database is a bad idea unless you know exactly what you are doing.

The {url_alias} table is written to with path_save().  If you look at the source, two hooks may be fired, depending on whether the path is new or update: hook_path_insert() or hook_path_update().

So, if you update  {url_alias} manually, you don't give any other modules the chance to react via the hooks.  Whether or not anything bad will happen depends on whether your system has any of these hooks in use.  Off the top of my head, I am unaware of any modules that do, but you would need to run a module_implements('path_insert') and module_implements('path_update') to be sure.

Your safest bet is to always use the API.  Write a standalone script, and execute it with drush -u 1 scr yourscrpt.php to make sure all of your hooks execute.