My goal here is to format the CF card as a bootableAmiga hard drive, so I can copy the hard
drive from my 600 to it, then put the CF in one of those IDE adapters and install it as the main hard drive.
This goal is quite difficult to achieve.
Firstly in order to make the card bootable you have to prepare it with HDToolbox.
The right command line is: hdtoolbox compactflash.device
compactflash.device must be in Devs: on the boot partition.
Now comes the difficult part. After saving changes in HDToolbox you have to reboot. On the IDE bus new partitions are automatically mounted after reboot. Compactflash.device does not do that. You have to find a utility which can mount partitions from a harddisk.
OS 3.9 comes with the Mounter utility which can do this. I am sure that similar utilities exist for OS 3.1, but I don't know of any.
Once the partitions are mounted you can format them and copy file to them.