If you suspect that a certain file is a dummy, then open the file in a hex editor. I use WinHex. If the file is completely made of empty data it will look a bit like the attached picture. In other words, it will be made completely of 00's. Make sure you scroll through the whole file and check it 'cause they sometimes start with 00's but have important data later on.
If you are absolutely certain that the whole file is completely made of 00's then you can probably get rid of it safely. If you do though, make sure you check that your new smaller .cdi runs correctly before deleting it.
I normally don't recommend doing things like this, but you asked.
The reason why I don't like it is this. You can't really be certain if this type of thing is safe to do though, because the dummy file may be used as a sort of key file by the game as a way of preventing modifications. In other words, the game may check if the dummy file exists and is the correct size or that the .cdi is a certain size. If the game determines that one of these checks turns out to be wrong then the game may then assume that you have modified the .cdi and deliberately not run/run incorrectly. This is an easy-to-implement form of protection used by programmers to stop people from messing with their hard work. I don't know whether these methods of protection were used on Dreamcast games, but they were used on some early PC games. The PC version of Geoff Crammond's Formula One Grand Prix 1 was one game I can think of that used a method like this. This game checks that there is exactly the right amount of free space on the floppy. If there isn't then it won't run.
Just a point to keep in mind when doing these types of things.
Hope this makes things clearer for you. :happy: