"hidden" file disappeared when Windows directory disappeared

I'm having a problem with my computer that has me mystified. I'm hoping you might be able to tell what the trouble is and how it might be remedied. My computer has had a recurring problem with the Windows directory "disappearing" (it's done it three times in as many years). When this happens, all of my display settings go away, my start menu changes, certain utilities have to be reloaded, etc. Those things are a nuisance, but this time it was much worse.

I have a folder containing hundreds of files of a project I'm working on for a patent application. A month or so ago, I got concerned about security, so I went into the "properties" of the folder and changed its "attributes" to "hidden". When the directory went away, suddenly my "hidden" folder went away too. I cannot seem to find or access it in any way; it's disappeared. I have some of the files backed up on floppy, but still, there are hundreds of files in that folder that I don't have anywhere else. Is there someway that I can retrieve this folder and its contents? Any suggestions would be greatly appreciated.

If it's useful, here's a rundown of my machine:
Compaq Armada 7400 laptop, 300K Pentium 2, Win98XE, 64 meg RAM.