Switch drive in SATA2, complete sync, switch SATA2 drive to SATA1, add new SATA2, sync succeed.
So I think the isw meta info probably lack identifier for either GRUB or dmraid to determine which one is the one with data, which one is the replaced drive.
The case in which it dropped me into ramfs I would assume that it's recognizing the empty drive as the drive with data and then wiped the drive with data empty after sync.
I still can't pin-point the problem but at least can narrow down the possibility so that if anyone see similar problem there's a procedure that won't wipe your entire drive.
We are glad that you found a workaround about this issue, we do not handle information about how Ubuntu handles it but if you have issues in the future we recommend you contact Ubuntu support for further assistance.