Unity doesn't have a track record of just deleting scenes. Obviously, it's possible (but unlikely) that there is a bug that caused this. It's maybe more likely that some AV software has taken a dislike to it and moved it into a secure, hidden area. If you do not have a regular backup, and you're unable to find the scene, then, I think you'll be out of luck. In which case, it's a lesson in how important backups are.
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