i did something like this,
i had a good 3.1 install with patches and stuff on one machine, pulled the hard disk out of the machine, plugged it into an IDE2USB adapter on my pc, fired up winuae, set the relevant options to mount the disk (it already has a disk file to boot from), copied over all the stuff off the hard disk to a draw/folder within the hardfile on winuae, removed the drive, plugged in the compact flash card, via same IDE USB adapter, partitioned/formatted and set as bootable, copied all the stuff from the backup draw to the new CF card/drive.
plugged CF card into amiga, all good.
bit of a convoluted way round, but i had three machines to do, and this seemed the quickest