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I usually lead with a Fakeout-U-Turn Ambipom, In one of my latest matches, Ambipom was OHKOed on the first turn and I changed to my Milktank. Later on in the match when I went to switch out and I noticed that I could switch into my Ambipom although it said that he had 0% HP left >.< I switched...

This is a Q about general pokemon games, Does using rare candies have any negative effects on your pokemon or Does using them as apposed to training cause them to be in anyway different to trained Pokemon (Excluding the fact that the won't have any EVs)