Disappearance

[Your Computer]

Yes.

The current story I'm working on is down there, along with a few invisible ones (not shown in normal custom stories folder) that I deleted. What to do?

Then it is possible your issue is related to the VirtualStore cache. Files get placed in the VirtualStore when the user doesn't have permission to modify the contents of the Program Files (and Windows) folder. This means Windows does something stupid with programs ran by the user. Instead of denying access, Windows lies to the programs and this may or may not cause issues. What you can do is run the Amnesia programs as administrator every time you want to use it, or you can "take ownership" of your custom story folder and see if that helps.