Note that this issue was also listed among the grievances in this question. This is a separate issue than splitting the monolithic project into a workspace (which is great), it appears that Product->Clean in Xcode also runs Clean unconditionally on the UE4 project included in the workspace, which causes critical engine files in /Users/Shared/UnrealEngine/4.10 to be removed.
As thejustinwalsh mentioned, the only way to recover from this is to run the Verify command in the Epic Games Launcher.