I see that we have replication enabled between the two nodes, but one of the VMs is only replicating half of its disks. Is there a solution to fix this?”
May we know more about the Disks? Or Perhaps get a PVE report? It is possible that only some of the Disk are stored on media that allows replication.
Report can be generated by going to DataCenter > Node > Subscription > Click System Report > Click Download