Are you working in a team on this project? Was anyone else in the edit session with you at the time.
I had it recently where me and a friend were working on a map together, and when I deleted one item, the game would delete about 20 other objects near it despite neither of us touching those. For example, I was building a custom skyscraper out of existing fortnite walls and experimenting with different types of walls. I’d delete one wall and then half the building would delete itself. This happened to me twice before we stopped trying to work on the project at the same time.
Once previously I loaded into one of my projects to find quite a lot of objects had deleted themselves between sessions some how.