It's probably the same situation as with the DBZ movies. Out of the three I've seen (the ones on CN), only "The Dead Zone" could be fit in with the continuity of the series. The other two couldn't possibly have happened, for reasons I will not go into here. They managed to avoid this with "Pokemon: The First Movie" by giving everyone amnesia, but apparently they couldn't find a way to disconnect the P2K with the series.
-With only a few small modifications, any canoe can travel through time!!!-
-Hooray! I have Mega-Ultra-Plus, for easier fun!!!!-
Pokey the Penguin