You do not need to bring your Vibe site down in order to perform backups. You might want to back up the Vibe file repository and the Vibe database every night, perhaps doing a full backup once a week and incremental backups on other days. You can back up the Lucene index whenever it is convenient. You can always reindex the Vibe site in order to re-create the Lucene index, but being able to restore one from backup can save time in case of an outage.