Yes you can. Search this forum for more info on it. It has been discussed here before.
Basically you connect your HD to your PC. Add the drive in the Winuae configuration window. You may need to disable the harddisk safety check (it's in the docs I guess and also discussed on this forum). Then you can access the drive from within the emulation. When you want to use HDToolbox you may need to change the ToolType in the icon to point to the correct device driver (it's not scsi.device but something else; I guess it's in the docs or somewhere on this forum).
You can then just install WB3.1 and swap the drive back to your Amiga.