Yes, they already said the ending will be different. Claude will probably recover his memories towards the end of the third season.
You could say the whole thing changed because they wanted Jennette to have more relevance. Basically, Jennette is the reason there is still no conclusion to this dreadful memory loss and the plot changed. All the novel readers are pissed and unsatisfied with how she took major parts of the plot (like, in the novel it was Claude the one who brought Athy back, and to give her space they erased VERY important Athy-Claude scenes). I'm one of them. I waited for the end of the season, but we are still stuck so I'm dropping this. I don't even care about the end anymore, seeing how Athy will have to do all the work saving everyone's sorry ass just to share things she worked hard for. And I hate how they changed things just to have Jennette play family in the end.
Am I the only one who's getting impatient? Like why is the amnesia arc so long? ╥﹏╥ When will Claude's memory come back? When will they discover the existence of dark claude? I'm just getting frustrated that the progress is sooooooooo slow. ┑( ̄Д  ̄)┍