A while ago all the virtual machines running on a Storage Spaces Direct cluster had in VMM the Unsupported Configuration status. First thing to do was to refresh the VM information, nothing changed. Then I went to check the Jobs for error and found this:
The highly available virtual machine is not supported by VMM because the virtual machine uses non-clustered storage.
Ensure that all of the files and pass-through disks belonging to the virtual machine reside on highly available storage.
From VMM I was not able to connect to the VMs or do anything else, also I noticed on Shared Volumes option from the cluster that the CSV was not present anymore. Thought that this is a VMM 2016 issue, so I updated to the latest one but issue was still there. I went to Failover Cluster Manager and there everything was looking ok, I was able to open and connect to the VMs, browse the CSV . The thing that was leading to an S2D issue was that the CSV had Warning at the Health Status and Operational Status was Degraded.
So I started to check the status of the Storage Spaces Direct. What I did first was to run Get-VirtualDisk which displayed me the Volume as Detached and with the Health Status Unknown and after that I ran Get-StorageJob command which was not displaying nothing at all. Something strange was happening.
Thanks to Jan-Tore Pedersen from the S2D slack community, who gave me the idea of moving the CSV on a different node, which fixed the issue. I did again the Get-StorageJob which showed that the Repair-Job was stuck and this was root cause of the issue.