Dont worry, hardware is meant to be used. when the hd fails you can also get a scsi2sd or a scsi card reader. If you dont want to lose workbench back it up to your 1200 just in case.
I had similar issues with my 2091 scsi controller, which wouldnt allow the a2000 to starr unless a cd was in the cdrom and the cdrom was not the final scsi unit.