you need a version.php file in your local/plugin folder. When going to the administration, this will trigger a Moodle update (everytime you bump this local plugin version.php). You should not need to bump the root version.php.
Moodle update process will update the web services found in core and in the plugins.
More information about version.php: http://docs.moodle.org/dev/version.php
PS: after reading again this discussion, are you saying that when you trigger a plugin update it does not update the plugin web service, and that you must trigger the bump version.php to properly update the web services? In this case it's a bug, you can report it on the Moodle Tracker
. Indicate what Moodle version you are using. Thanks.