Ok I gave you this advice before: install OS3.1 in Winuae on your HD. That way you have a fully booting HD which you can use in your Amiga again.
If you copy the adf files onto your HD and some tools to write them back to disk (look on Aminet for some tools like adfblitzer or adf2disk). Then you can use your real Amiga to write the adfs to disk.
