Well, I can forgive the Animarium/freezing/etcetera thing as being magic - since it was raised using magic, it just makes sense to also use magic to keep it obscured or forgotten about, and life-sustaining for the sake of the sleeping princess. But Cole getting to (land-locked) Turtle Cove in Colorado (which is where Word of God has said Turtle Cove is) with a pole raft when he started out from most likely Brazil (where there is somehow a chimpanzee)... Yeah. There are some details that you really have to forgive or your brain will break.

The way I figure it, Merrick probably made himself a new flute, though, because Zen-Aku had a flute already. They never explain how Zen-Aku came back the second time, though, what with his horn broken.