Dont know about the Acer Setup but when I used the recover disc I built I went back to what was shipped - tried this just after I got the box to check what would happen before I started using it. I would guess you will end up back with a massive C: drive and no E: partition.
I used Gparted click here to re-partition as I couldnt get the vista ptn below 120Gb using its own tool - because of in-use files. Now down to 30Gb and anything that isnt a program or OS is on another ptn.
I Image the C: drive to a backup ptn, so I am hoping the need to go back to factory settings will only be if I take a huge hit or have to replace the HDD