Backup Catalog saves only the active catalog. The active catalog does not know anything about other catalogs.
You have to backup all your catalogs individually (which is one of many reasons why having only one catalog is a better way to go)
Depending on where you choose to have the backup written to, it may or may not overwrite the previous one.
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When you use the command File à Backup Catalog to CD DVD or External Hard Drive
Elements will work on the open catalog as indicated by the catalog name (bottom left of Organizer)