Aditya,
I understand your concern. Completely. It makes total sense that you want to ensure that you stay ethical and that you don't submit a project when you should not.
Therefore, I signed on the PMI chat and the person I spoke to (Pawan) confirmed that there is no problem in re-submitting a project from your PMP application also on your PMI-ACP application.
I pressed on and asked: "To confirm: It is OK for my student to submit an agile/hybrid project for agile experience in the PMI-ACP exam, even if this project had previously already been submitted for the PMP exam?". And that is when the chat crashed and I got disconnected... ARGH!
So... I would, therefore, recommend that you try chatting with them yourself for a final confirmation. Please visit
www.pmi.org/about/contact
and click on the chat button.