I think a possible solution to your issue is adding entries to ActiveStructRedirects or ActiveClassRedirects in DefaultEngine.ini.
You’ll need to know both the old and new names for each class and struct. I don’t know the old names so I couldn’t test it.
You can look at Intermediate/Config/CoalescedSourceConfigs/Engine.ini to see what the format of the entry should be like.
It’s not that you should never rename files in UE4, it’s that you need to do so carefully and make sure the engine knows where to find the new resource.