Retraining essentially lets you repick feats that you took earlier. It allow me to qualify for Divine Prankster one level early by taking the Favored and Primary Contact feats to get 1 bonus skill rank, and then swap those feats later on when I qualified for the PrC outright.
Basically it's the difference between my build being Cleric 4/Divine Prankster 3/ScM 3 vs Cleric 5/DP 2/ScM 3.