Nethserver supports KVM/qemu with web UI, so you may replace your Ubuntu to have physical and virtual Nethservers
You are able to replicate only what changed, In KVM/qemu there is block replication.
VMWare supports CBT(Changed Block Tracking)
Proxmox has storage replication
That would be possible with the virtual hard disks, just make os disks and data disks, so you may backup them differently, like data every day and os less frequently. But when able to just backup what changed, you may even do it everyday without problems.