Another thing to add is that I'm using SFS - Is it possible that I only have SFS installed in the IDE HDD's RDB and thats enough for the SCSI HDD to work when the IDE is in?
Thats exact the explanation. The Kickstart ROM contains the FFS-Filesystem, so you can boot from any bootable FFS-Partititon without having to have the filesystem in the RDB of the Disk.
I assume you have the SFS-filesystem in the RDB of the IDE-disk so the Amiga is aware of it and can boot the SFS formated SCSI-Disk.
All you have to do is add the SFS filesystem to the RDB of the SCSI disk and you are set.
To do this open the HDToolbox select the SCSI-Disk, select partition and the click down right on add/update to add the SFS-filesystem. You should find the filesystem in the L drawer of your system partition.
After you have added the SFS filesyystem save the changes to the drive and exit HD-Toolbox. That`s it.