I also encounter this issue with the manually compiled version of Unreal Engine, and the only fix i found for now was to manually retrieve all the missing include and source folders and manually add them in the IncludePath and SourcePath of my .vcxproj file.
Here’s the python script i used for anyone interested:
import pathlib
import os
# Replace the content between the quotes with the path to your UnrealEngine's `Engine/Source/Runtime` folder
base_source_runtime = pathlib.Path("E:\\UnrealEngine\\Engine\\Source\\Runtime")
# Same thing with the path to your UnrealEngine's `Engine/Plugins` folder
base_plugin = pathlib.Path("E:\\UnrealEngine\\Engine\\Plugins")
with open("includes_plugins.txt", "w") as f:
f.write(";".join([str(pu) for pu in set([p.parent for p in base_plugin.rglob("*.cpp")])]))
with open("includes_source_runtime.txt", "w") as f:
f.write(";".join([str(pu) for pu in set([p.parent for p in base_source_runtime .rglob("*.cpp")])]))
Then you need to add the long line from the includes_source_runtime.txt and the long line from the includes_plugins.txt, that were just created, in the IncludePath and SourcePath sections of your .vcxproj file for your project.
That seems really dirty, but it seems to work. I also couldn’t find a better way to fix this, after searching the internet for a while.