i said "almost the same bug" because the old v5 Curse Client would also blindly overwrite folders and files belonging to an addon (in my case it was the 2016 versions of Swatter and SlideBar from Auctioneer) with older versions of those that were delivered with other addons (2014 versions of Swatter, SlideBar from Gatherer - the updated version of Gatherer for Legion was not released at that time. The 2014 one was the most recent.)
since the deletion bug still happens in Curse App, i assume that the folder overwrite bug might also be present too, since they are related... don't have time to test it at the moment though. maybe tomorrow.
at the time i thought it was a bug with Auctioneer and/or Gatherer
quotes from march 2016:
using Curse Client, today i decided to uninstall Gatherer but keep Auctioneer Suite... after uninstalling Gatherer and going back into WoW i found that Swatter and SlideBar have also been nuked, even though they are components of Auctioneer
digging deeper into this i discovered that Gatherer also includes them as components and Curse Client uninstalled them because it considered them as belonging to Gatherer rather than to Auctioneer Suite. They both contain different versions of Swatter and SlideBar... and whichever gets installed last will overwrite the other one's files.