The agent operates independent of other applications. The agent for Arcserve Backup backs up open files without disturbing an application; an application can write to its files when a backup job is running without having to communicate with the agent at all.
Using the agent for backing up is the only way to guarantee that all open files, including those that are not associated with a Writer, will be reliably backed up. If open files that are not associated with a Writer are backed up using VSS, there is no guarantee of transactional integrity and you will run the risk of invalidating the entire backup.
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