There are a few easy ways to do this

Put the Amiga drive in a Windows computer, run WinUAE and configure to your liking then just go to the "CD & Hard drives" option, press "Add Hard Drive" (don't forget to run WinUAE as admin) and then just press "create hard disk image file" and you have a clone of your drive safe and sound

Later if you go for a new HDD or a CF solution you just have to mount both the HDF file and the new drive and then prepare the new drive it in hdtoolbox, don't forget to edit tooltypes to uaehf.device and don't forget to set maxtransfer to 0x1FE00 after that just copy everything over to the new drive and you are done.
Good luck

Edit: someone posted while I was typing
