Hello
Converter creates a separate virtual disk for LVM volume groups but keeps the /boot volume as basic volume. That's why you had 2 virtual disks. This is normal and expected.
As for the reconfiguration error - you ought to post the logs for someone to be able to have an idea was has gone wrong.
You can also try again to manually rebuild initrd image, but do not uncheck the reconfigure option. If the error is during reconfig, then all the data have been successfully copied. OTOH reconfig does more than rebuilding initrd image (e.g. patch /etc/fstab) which you have missed.
HTH
Plamen