I license a game engine so have to use a compiled exe to run my app.
I know about a line of code in the source that is causing a lot of unnecessary compute overhead (I have the source but cannot compile myself due to other libraries included in my current licensed exe).
How can modify the .exe to comment out one particular line. Or unset a particular #define?
You can't. For a native C++ application, when a executable is created, all that's left are the assembly instructions. The best you can do is some reverse-engineering with the assembly to pinpoint which instructions you want to remove or modify (and I don't know the specifics of low-level assembly). Probably easier to re-compile.