According to splunk official deployment server documentation (5.0.2) if you do change to a serverclass.conf you need a full restart BUT if you only update a file within an deployed app then its a "splunk reload deploy-server" (no class flag specified so it should check EVERYTHING).
When you first configure the deployment server, and whenever you update its configuration by editing serverclass.conf, you'll need to restart or reload it for the changes to take effect. The clients will then pick up any new or changed content. Instead of restarting the server, you can use the CLI reload deploy-server command. - source : http://docs.splunk.com/Documentation/Splunk/5.0.2/Deploy/Updateconfigurations
I am however finding that updating of an app (edit of an existing and addition of an entirely new file) and issuing the reload command doesn't actually refresh/update the tar bundles within the $SPLUNK_HOME/var/run/tmp dir. The bundles still have the same time stamps and also epoch times in their file names.
I'm 100% sure this works fine in v4 as we utilise a cron scheduled reload deploy-server command to auto refresh our apps when they are updated.
I've tried running the reload command with "-debug" but it doesn't really give much insight into what is actually occuring.
Note: Yes I know a full splunk restart will create the bundles with the updated changes. Yes I realise this is a work around but I don't want to be bouncing splunk every 10 mins to replicate app changes around. It's feeling like a bug or something I have totally missed in the v4->v5 change.