How to create archives on Linux which support replacing/deleting files?
I think you should seriously consider using ZFS or any other advanced file system. This will allow you to
- create incremental backups (via snapshots)
- modify files within backups
- manage everything via command line (cronjobs etc.)
- use compression
- move backups across devices
- use different RAID levels if you need more security
ZFS runs perfectly under Solaris, but there is already a stable port for Linux.