I don't remember this EVER happening before with the CK tool. It wasn't just the Skyrim base folders and files either, it was a near clean wipe (for example, all SKSE files were also wiped; only a few files in the data folder are left).

The CK wasn't opening so I thought to verify the files. That didn't work so I uninstalled and reinstalled the CK tool only (right-clicked it from the tool list), but found it still not working. Only then did I find out my whole skyrim folder was wiped so naturally the CK couldn't find the 'executable'. That wasn't the only thing it couldn't find...

So I have to re-download the whole game, 6 GB, because of this...

Thank gawd that I use Mod Organizer so all my mods are organized OUTSIDE the main folders, otherwise it'll be a much, much bigger inconvenience and I'd be a lot more peeved.

Still, what the heck is up with this? And not even a passing warning?

I'd reported this during the beta, but others were unable to reproduce it. My Steam\SteamApps\Common\Skyrim folder is a SymLink to my real installation directory, so the Skyrim directory being deleted, thankfully, just necessitated creating a new SymLink. Might want to do something similar just in case.