For Master server, make sure you install 6.0 MP5 on new server and perform a catalog recovery before upgrading to 6.5.
Due to changes in the structure of the NetBackup catalog, it is not possible to restore a NetBackup catalog from a more recent NetBackup Maintenance Pack (such as NetBackup 6.0 MP2) to an earlier version of NetBackup (such as NetBackup 6.0 MP1).
To resolve this issue, remove the more recent NetBackup Maintenance Pack, reinstall the older NetBackup Maintenance Pack, and recover the catalog. After successfully restoring the catalog, then upgrade the server to the desired NetBackup Maintenance Pack. Please be sure all graphical user interfaces (GUIs) are closed before starting the patch process.
Following flow chart in addition to Admin and troubleshooting guide for catalog recover will be helpful.
You do not need to do anything for media server, since all of the media related information is now stored in EMM db. Just install new media server and add it to master.