Finally after half year I fixed it. The filesystem had error. I did:

• downloaded ubuntu iso on host machine
• attached iso as CD-ROM
• turned off UEFI
• turned off boot from hard drive
• set up CD-ROM as first device to boot
• started virtual machine and selected boot from CD-ROM
• after ubuntu started I launched gparted, selected disk with HA and run check/fix on data partition (twice)
• powered off virtual device
• unchecked boot from CD-ROM, checked boot from HD and moved it to first position
• moved HD in boot order to top
• started the virtual machine. no Ctrl-D was required

Source: UPDATE – System OS to 6.0 – Home Assistant OS – Home Assistant Community