I just updated CCleaner and ran it, the result of which was my list of files for Acrobat Reader disappeared and my uTorrent torrents disappeared. I've since gone through the Windows and Applications tabs and unchecked things that were strangely checked by default including, under the Windows tab, "Last Download Location." On many browsers, etc. remembering the last download location is something the user intentionally chooses among the options.
The files involved are a tiny amount of the normal file cleanup and wouldn't have much effect on users to keep.
CC has always targeted junk, temp, crap, and personal history categories of files, to name the main-stayers.
a lot of CC users predominantly run it to remove their usage tracks, be it browser based or most recent used files.
I guess this is a good example of checking the default settings for any software before blindly running it, especially a piece of kit that will be cleansing your system.
glad you found the cause and it won't happen again.
and as you say, luckily they were only trivial data.