This is very alarming. Today after syncing the project all of the assets we have ever deleted have come back - these include actors, landscapes, devices, static meshes, materials, sound and cue files, etc.
This issue can be closed for now. After inspection it was oneDrive, the file backup system of windows reintroducing old files into the project. We will be working with the editor team to provide a warning when the user has their project files situated within a folder that is backed up by an external system.