If you have a sitatuion like
Public/Filename/Foo.h
Public/FileName/Bar.h
you cannot have
#include "Foo.h"
#include "Bar.h"
in your .cpp file during the native build. Either Foo.h or Bar.h will be missing because UBT will only add one of the above directories to the includes.
Build FortniteServer natively.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-37174 in the post.