Yes. It'll infest all of your data files and rewrite the same data to those files, making them identical, but you'll know that the data was changed. Therefore all of those files become worthless and need to be deleted. After that, it hops out of your hard drive and into your Pokemon game catridge's ROM and removes all code related to PID randomness. All following PIDs will be written as 0xBADBAD. Code will also be injected to overwrite all existing PIDs in the save file with that value. Finally, it changes your character's name to "CARESABOUTPIDS", by modifying the game code to allow that length of a name.
Edit: I feel pathetic typing this because it shouldn't be necessary. There is nothing in PokeGen that could possibly affect your computer or DS in a negative way.