I gave them my old I-94 (the one I got when I first entered USA, not H1B I-94), before I left USA.
When I entered USA again using AP, they stamped my I-94 with AOS.
When I applied for my H1B transfer, I submitted a copy of my AOS I-94 to USCIS. It seemed that they didn't question about the AOS.
Hope the info helps. The issue is in debate, since nobody can present an official document to clarify it. Anyway, good luck to you and all of us. USCIS, esp. NSC really sucks.