Few days ago friend of mine asked me if I know how to fix this issue and I succeeded. Now I want to share with all of you.
The scenario is as follows…

Windows Server 2012 R2, one Storage Pool, few virtual disks. The behavior starts to happen after Windows Server 2012 R2 re-installation. Everything was fine until restart. Virtual Disks are present and attached but after restart the server they are detached.

Before restart.

After restart.

If you are looking under virtual disk Properties/Details/Property (look picture below) you will notice that IsManualAttach – Value is True. In other words, if you want virtual disk be attached you must do manually attach.

Resolution

Open PowerShell as administrator, type as follows and press Enter

Set-virtualdisk -FriendlyName <VirtualDiskName> -IsManualAttach $false

Refresh Server Manager Console and you Virtual Disks will be attached. After you restart your server Virtual Disks still be attached .