Well, if you stop backuppc with "service backuppc stop" this will also stop all backups that are in progress.
If you are using "rsync" as your backup method, then the backup will be saved as a "partial" backup, and it will continue when backuppc is started again.
Now, if you just want restart backuppc gracefully so that it may recognize any changes that you may have done to the config file, then you should use "service backuppc reload". This will cause backuppc to be restarted gracefully and no backups that are in progress will be stopped.