This just happened to me:
Realised I meant to click "Remove folder from project".
Too late. All gone.
The best part is this: it was a version-controlled project folder, but ST3 even deleted the .git subdirectory.
A single click for a recursive delete operation, with no prompt, and no way to reverse it afterwards? In a context menu that also contains a similarly named non-destructive operation which is used frequently?
Customer support service by UserEcho