I didn't check what the docs say exactly. By pressing S you disable the SCSI controller, so your drives are not mounted and cannot show in the early startup menu.
You can also hold down A which will disable the CSPPC alltogether.
The important point in disabling anything is to ensure that no part of the firmware is in use while you update it.
So if you press S and don't see your SCSI harddrives in the early start menu, everything is fine. Then click on "boot without startup sequence" and run the update from floppy disk (or from IDE HDD).