I've tried that. SCSIBootSel can see both harddrives, but no matter what i select, it still boots from the first one it finds.
A have a 700 mb drive mounted in the controller's box at id 6, with WB 2.0, and the 100 mb drive, that came with the Amiga, when i brought it second hand in external box with id 2 and a trashed WB 1.3, where nothing works. But i would like to transfer the HD installed games from the 100 mb drive, without having to use floppys or transfer everything over the serial port.