Portable Apps Folder is empty, and so is the Documents folder!

I popped in my flash drive after not messing with it in a while, i usually use my other one, and for some reason the portable apps suite wont start up so i went into the directory folder but its empty and so is the document folder, if i click on properties it shows it as being 0 kb, while if i do the properties of the USB its the same size as it was before. I am able to see hidden folders as well as system ones but the folders remain empty. I have no clue as what to do now. Any help would be greatly appreciated. Thanks.