It would make the NEW drive match the emulated drive. That means if the emulated drive has a corrupt file system then the rebuilt drive will also have a corrupt file system. That is why I said you should be trying to repair the file system on the emulated drive(s), and it is recommended that you do this before attempting a rebuild.
The disabled drives may actually be fine - have you tried unassigning them and then seeing if it mounts in Unassigned Devices?