it's seems that update removed some PAM modules - some were replaced by different ones. So yeah, it's a mess. In worst case scenario I'll install new version in another VM and will try switching the volumes.
edit: so my plan worked. I've stopped VM with OMV . I've downloaded the new installer image and uploaded to my Proxmox instance and created a new VM for the updated OMV version. I didn't start it immediately though - I've opened Proxmox shell, renamed the drive used for samba in the old, so it would match newly created VM name. Then I've edited the config file for the new one and added this drive.
Moving disk image from one KVM machine to another - Proxmox VE
With that done I've launched the VM and proceeded with install and adding the old share.