some spoiler questions I saw asked in the last page or so...
regarding the dead guy in the lighthouse in the beginning of the game...he was killed by the Lutece's...a map is shown later in the game which shows that the Lutece's considered him the final loose end (or something along those lines)...as far as the disappearing Elizabeths in the end of the game...all Elizabeth's die...once Comstock ceases to exist then so does Elizabeth...Comstock created her hence she cannot live without his existence...Anna lives on but since she was never taken by Comstock she can never become Elizabeth