Yes you could do that. If you decide to go with good old WB3.1 or ClassicWB then try this...
Boot your WB3.1 floppy. Start HDToolBox, click "Change Drive Type", click "Define New", click "Read Configuration" (the size won't match, just ignore it), click "Ok". click "Ok". Now click "Partition Drive", click "New Partition", create just one 500MB partition, you can use filesystem at will, I used PFS3. Here is a PFS3 guide with tutorial for libs, IDs etc:
http://grimore.org/amiga/compact_flash
Don't create other partitions yet, all you need is just one for WB at this point. Quick-format the partition using appropriate command line tool (for PFS3 see the guide mentioned above).
Copy everything from your mechanical drive's WB partition to this newly created partition.
Reboot your Amiga, it should boot fine.
Now you need to add the updated scsi.device. I've used 43.45 which came with ClassicWB in MyFiles/LargeHD/128GB_Support/SCSI_v43_45_ChrisToni. Copy A1200IDE.scsi.device.43.45 to Devs: and rename it to scsi.device. Add the following to the top of the S:Startup-Sequence:
Code:
IF EXISTS DEVS:scsi.device
C:LoadModule DEVS:scsi.device
EndIF
Now reboot your Amiga and verify the updated scsi.device is loaded. Open the shell and type "version scsi.device", it should reply with "scsi.device 43.45".
If everything is ok, proceed to HDToolBox and create and quick-format other partition(s) at will.
At the end, verify that everything is fine using Check4GB command line tool. It should look like this:
