When upgrading your project, we always suggest using the open-a-copy unless your hard drive space is very limited. The route you took is very ‘custom’ and is definitely going to cause some issues.
Open up your project through the launcher, select the engine version, and press the launch option. Then select the project you wish to update (Grayed-out if not current engine version).
Upgrading Project
Unfortunately, since you have gone about upgrading you project in a unique fashion, reproducing the issue you are experiencing is going to be difficult. In the future, keep this option in mind. If you still have a copy of your original, you can use this suggested route and let me know if your lighting is still broken.
Thank you,