I've managed to reproduce it. It does look like a bug but actually it is not so important as it looks. Reconfiguration affects only the system volume, the others are not changed by it.
I thought the resulting VM (along with the disk) would be deleted but it was not. Is it the case with your machine too?
If the disk is there, it means the data have been cloned and you can proceed with joining the vmdk to the other machine. Of course, as mentioned above, you can't do synchronization in this case.
I hope running a single conversion with (almost) all volumes will succeed. POCEH suggested also to try parallel disk cloning (Go to Administration menu, then "Data connections per task"). This is rather a shot in the dark but it might help.
Regards