The two sentences indeed have different meanings, the first one implies that you know for a fact that the island has disapeared. You would use it for example navigating your boat at the exact place the island should be, and it isn’t ; when the second one only implies that you don’t understand the process, you would use it for example if one of your marine come back from the said island only to tell you it isn’t here anymore.

About your additional questions, bien only emphasis on the absurdity of the statement, it’s a little bit like “how on earth [..] ?” As to the order of the words, I think both are correct. “Bien” after the verb is a little more oldschool.

Cheers

The first sentence is in passé composé, it means you are talking about events that happened relatively close in the past. Here you are confronted to the vanishing of the island and wonder how it happened.

The second sentence is in conditionnel, it means you are talking about hypothetical events. Here someone told you the island vanished but as you can’t think about how it could have happened you can’t really believe him.

Additional questions:

“Bien” can be used for really many things in French. The construction “Comment X a-t-il bien pu faire Y ?” is an expression figée and this use of “bien” is pretty unique. The meaning is the same as “Comment X a-t-il pu faire Y ?” but it makes the sentence more emotional.

If you move “bien”, you are breaking this expression figée, and so the meaning becomes different: “Comment X a-t-il pu bien faire Y ?” means that you are wondering how X proceeded to do Y well.

“Comment a-t-il pu” is used when you talk about an action that lies in the past and which actually happened.

“Comment aurait-il pu” is used to describe an action that could have been the case but never happened.

For example: If you studied harder you would have passed the exam.