-device vfio-pci,host=0000:05:00.0,id=hostdev1,bus=pci.0,addr=0x9 \
05:00.0 RAID bus controller [0104]: Broadcom / LSI SAS2008 PCI-Express Fusion-MPT SAS-2 [Falcon] [1000:0072] (rev 03)
Subsystem: Fujitsu Technology Solutions HBA Ctrl SAS 6G 0/1 [D2607] [1734:1177]
Kernel driver in use: mpt3sas
Kernel modules: mpt3sas
The LSI is being passed though to the VM, so when you start it Unraid loses access to it and the disks.