After several weeks of searching for why my files would disappear after booting into Windows 8 I found out why. I have a Media partition that I use to store my music, pictures, videos, movies, documents, downloads, and pretty much anything I want on both OS's. It was fine when using Windows 7, but Windows 8 has a new way of shutting down. It puts itself into a hybrid hibernation/off state. While this makes boot times extremely fast (less than 10 seconds on a HDD) it deletes all my files because it's restoring it to the pre-hibernation state. (Explained better here.) I'm doing this as a warning to anybody else planning on, or that is currently dual-booting Windows 8 with any other OS. Instead of shutting down, restart. The boot times are longer, but it's better than losing several hours of hard work.