Mta,
Yes, the files are still technically there, but they don't open correctly when trying to open them with Computer or Illustrator File>Open. When I try to open one of them, Illustrator apparently thinks it's a text document and gives me a "Text Import Options" box. If I say 'ok' to that, the document opens but it is completely blank.
I did some more tests and actually I can NOT open many old files that were on a thumb drive and not on the system that I CCleaned. It appears that if the image does not contain a linked file, it does open, but if it does contain a linked file. it doesn't open right. When opening old files that were not on the system Illustrator does not give me the Text Options Box, but it does give me numerous repeated messages: "Could not find a plug-in to read the linked file (a .jpg background in the image). After several repeats of this window in which I choose either 'replace image' or 'ignore', the file opens without the linked .jpgs and then gives me another box: "Could not read the file because the plug-in could not understand this file". When I click 'ok', the document closes. In some tests I received the latter message ("Could not read the file because the plug-in could not understand this file") without the previous windows.
Yes, I can create a new document, save it and re-open it fine.
When I tried to open with 'computer' I did choose Computer>Open With>Choose Default Program.
Yes, I think it ran the registry cleaner too.
What do you think?