Aeris' materia should be put back into your inventory. I'm pretty sure I had summons on her at the end of Disc 1 and I still got the master summon. As for the Choco/Mog summon materia, I think you can pick that up any time. Just talk to the chocobos at the Chocobo Farm.

Edit: Ah, I be wrong about Choco/Mog, it seems! I agree with the equipment on Aeris being lost but I think you still keep the materia.