If you ignore overprint, then you should be ok.
If a file as overprint setting in them, which is usually for press printing, and you don't ignore them, you will get screwed up colors.
Let's say that you are printing black text over a picture. In press printing with no overprint, the rip will put white "holes" in the picture for the black to go in. With overprint, the black will go over the colors, the rip won't leave white for the black.
Does this make sense?