I have been playing planescape for a while with no problems at all, and then one time I go to load my game and all the saves are missing. I looked on this forum and found the appdata folder that should hold the saves and they were right there, but the game still does not recognize them. How do I fix this?

The only other thing I can think of that might affect it is, since I had some IE nostalgia from playing pst, I got baulder's gate and was installing that super big world mod thing for that, could it have somehow affected planescape? I definitely installed the big world project in the right location, but both planescape and BG2 are in the GOG folder in my program files

bwp won't affect PST
did you recently turn off Microsoft User Account Control?
or start launching the game from a different shortcut...

copy and paste the saved games from "appdata" to torment's "save" folder
then make sure you always run the game as an administrator (right-click on torment.exe)

OR

install the game to outside the "Program Files" folder as ALL the mods tell you to do