Some do, some don't. I know when the Corpus Christi EM program started up, they took folks from a program that had closed. Another program that opened recently - UWisconsin - didn't take any upperclassmen. Some specialties have rules as to how long you have to be at the program you graduate from, though. I think for FP it's 2 years - which would mean anyone transferring would have to repeat a year.