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If Air was anything to go by, the last two episodes will probably just be fanservice or filler or something. The last two episodes in Air were called, "Air in Summer," and they expanded on something that they didn't in the anime.
Well, the last two definitely won't be the After Story. Maybe it'll be a part in the game that they didn't think would completely flow with the anime [maybe mess up the flow?], but a part that they wanted to animate anyways.
Edit: It seems I didn't completely understand what you guys meant. Too lazy to edit the entire post though.