Actually, Codetapper has discussed this in a different thread (sorry I don't have it handy, but hopefully one of the thread-location fetishists will help you out here). But it is not really uncommon in games. I was just looking at a copy of European Championship '92 and disk 1 appeared to be DOS (although with no files) and disk 2 was NDOS.
I don't recommend filecopying any commercial games, btw. DMS on an Amiga or zipped adf's on the PC.