When files download, and I hit Clear Inactive, the files do not go into a certain folder, they just disappear. I've looked all through the folders to find them, but they just aren't there. I know they're downloaded because everytime, I try to download the same files, it asks me if I want to replace these files. Where could they be? Please someone help!

Look in the Options to see the folder you set for completed downloads, or just search your hard drive for the name of one of those files. If you set your Completed folder to NOT share, it won't show in you Library, but is still on your hard drive. You can add it back to the Library by choosing Library->File->Add Folder to Share once you know where it is.