HD drive is not very reliable, a replacement will set you back 100 USD if you want an original and about 30 for a new one which is just a hacked pc drive, which will probably not let you boot non-dos games from floppy that use a particular signal not present - example of this would be Cannon Fodder.
Wear and tear on the HD floppy is not very recommended. I would be using an external drive if I were you.
And yes, there is such a program. It is called ADF2DISK and is available on aminet.
Here's how you use it: adf2disk filename.adf
This will write the adf to df0, which does not need to be formatted - however it is a good idea to format the disks in x-copy so you can check disk integrity, because after 20-30 years these disks start deteriorating.
If on the other hand you want to write to DF1: then it is a little more complicated.
From what I remember you have to use the following command:
adf2disk filename.adf trackdisk.device 1
That will then write the adf using the trackdisk.device (floppy) and unit 1, which will be the external. Unit 0 would be the internal. And so on.
Hope this helps.
Edit: I now notice I was answering the wrong question, which you did not ask :-D
Anyhow, what you can do is use the adf to dms converter and then convert the adf files to dms, and then extract to harddrive like you wanted.
