Whenever you update the Engine version that your project is running on, you likely also need to explicitly re-save many of your project assets. Many types of asset will have Engine-specific data saved in them. Though they will technically work if you open the project in an Editor of a different Engine version, they will have very slow startup times unless/until you explicitly re-save them using the new Engine.

Not UE-specific, but a very nice profiling tool that can be used with UE for more precise stats.