Which version of Call Manager?
If 3.3(3), and/or 4.x then BARS is the backup program. BARS stores 3 backup tar files by default in the storage location along with 7 backup log/trace files. The number of files kept can be increased or decreased in BARS as well as number of log files. But, once the backup tar file is made you can do whatever you want with it. You can back the storage location (usually a mapped drive) up to tape, put it on your NAS, etc and treat it like other server backup and data your organization backs up and maintains.
Call Manager 5.x has different backup application, that uses SFTP to copy backup to a SFTP server and same concepts apply. Once the data is on storage server (SFTP in this case) it is yours to handle how you need to.
The backup application just backs up the data, not the applications or OS.
HTH, Erick