When that happens to me, I do a new install on another HDD. Make the new HDD the boot. Then the new install should see all the folders on he old HDD after you do the option to show everything.
After that, migrate important stuff to the new drive. Do not format the old drive. Keep it around until you are sure there is nothing on it you need. That might take a year. But for the present cost of a spare HDD it is good insurance.
heh, that's what I do. I Still have a working 50MB boot drive from my 386. Hey, you never know when I might need something off it.
I have at least 5 or 6 copies of most of my important stuff on various hard drives, at various stages of development, too. But that's simply a side effect of that nervous feeling I get when I go to format one "Is there anything I missed?".
Of course being that I copy the entire contents I can't see how I would miss something... but the feeling persists nonetheless.