I don't have a save game near there, nor time to try right now, but a quick guess would be that she needs to be placed on the walkmesh, so you could try removing Cait Sith for example and using his XYZI in Aeris' script. Failing that, change Cait one part at a time into Aeris (first model, then bits of script) to see which change is causing her disappearance.