Hello NoaScape,
There are a few possibilities that come to mind regarding the shadow flickering. I have a few questions to clarify a few suspicions I have.
1.) Are you using a FOV that is non default. Within 4.9 there was a bug reported that turned the screen black if a FOV different than 90 and " Cast Modulated Shadows " was used. This bug was fixed as of 4.10.
2.) Does Switching to LDR resolve this issue?
3.) Please be sure that all of your textures and light maps are a power of 2.
4.) Have you tried launching or packaging using 4.10? If not would you test an asset that is giving you this issue within a test project using the same lighting and shadows that you are in your 4.9 project.
After completing these troubleshoots please post again with the results of each one.