This is a known issue (as noted in the notes for the firmware update).
I have not debugged what exactly is causing it but I think u-boot does not properly reset and rescan the drives on a warm reboot. It does not appear to be an issue with Linux, if you boot into recovery firmware or from another device (like NVMe) they come up correctly.
My suggestion would be to use another type of boot device (like a 22x42 M.2 in the Key B, or USB drive) for now.
(and definitely in the case of muvirt you can have your VM data on the SATA drives rather than the device you’re booting from)