It seems the latest CC is deleting the contents of the first invisible folder on the top level of the HD. On my system, this happens to be a folder created by BackBlaze backup service.
Here is the tech note: https://backblaze.zendesk.com/entries/98786348
Why on earth is CC deleting contents on a folder it did not create? Note that it seems to affect ANY first folder, not just the back blaze one, so if you have any other installation it might mess with that as well.