Delete the old, exit/save changes, reboot, then try to re-add? AFAIR HDToolbox doesn't actually save the changes to the partition table / RDB until you exit.
If you're worried about it hosing your existing partition, take it out of the equation altogether - boot from a 3.1 or 3.9 floppy with your primary partition completely disconnected and prep it that way.
I'm assuming the SCSI2SD thingy isn't somehow interfering with the Amiga being able to read the correct drive geometry.
Also, what the heck do you have going on in this picture? :laughing: