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No, that method isn't just for the 25 empty spaces, it works for any used Pokemon as well.
I also probably won't be appearing on MSN again for a while, I have exams at the moment so I need to focus on those. I will still be logging on to PC everyday though.
I'm a little confused. Do you mean one of the empty "???" Pokemon after Celebi?
You can't delete them but you can get rid of the sprite by going to 800000 and filling every byte with FF. I don't recommend you try this if you've got any data past 800000 because that could cause problems in your rom.