Depends on the program. Some programs don't recalculate GPA at all, some may take into account classes you repeated and some may not. All programs, however, are going to require all of your transcripts. They don't look at your GPA in isolation - they look at it with respect to the program of study you undertook. So having a 3.4 won't matter if you have a 2.5 in all your history classes, and your As came from general electives, for example.
How many classes did you repeat? If it's just 1 or 2, that's fine, but more than that starts to look strange.