We have limited space for our backups to disk so we do not want to backup the whole server. I export all the policys to get backed up to disk. What other folders/files should I backup. My recovery would be to rebuild the server install EPO again, then recover all folders/files I backup to disk.
Please see McAfee support article KB66616 - ePO 4.5 and 4.6 server backup and disaster recovery procedure
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The article lists everything required.