I have looking around a bit, and have had no luck with this. I have found programs than will simply extract ADFs. Some games and stuff for the Amiga though weren't recognise through the Amiga os, the could only be accessed once by the game once the game was started. Example: Super Star Dust- You had to boot off
install disk to make a special install disk, after that you restarted with this new disk and ran the program, it was able to get the files off the disk, but that was the only
way.

Finally to the point as I have some ADFs taken off disks like this can't simply be extracted, is there a way to turn it into a DMS, because most DMS files will format a disk themselves and in these strange formats the Amiga doesn't regularly recognize. Or is there another way around this?

Well I'm not sure I understood your question perfectly, but if your problem is that the Amiga won't write ADF files properly to disks (Extracting to disk) then you might want to find another disk extractor.

I use ADFBlitzer (Which I found on ALE) which will usually handle strange file sizes (Enabled me to write Click Clack which was a little bigger than most game disks). Problem with this program is that it doesn't check the disk for errors while writing.

Because of this I usually use a program called DIP (I think I got it from AmiNet) which verify the disk as it writes.

Both these programs blank the disk before writing.

I hope that this helps you, and that some of the information I posted was something you need.