In the screenshot you posted you can see the disks/volumes which contain VMFS partitions (datastore). Those are marked with an asterik on the left.
Installing ESXi on the IDSDM should only overwrite the SD device, and shouldn't touch the other disks. After installing and configuring ESXi you can then use the Datastore Browser from the vSphere Client, and right-click the different VMs' configuration (.vmx) files in order to add them back to the host's inventory again.
The Update option doesn't help much in your case, as it won't allow to enter a new root password.
André