I was able to somewhat reproduce it by:
1) create a .h such as C:\debug.h with #define C_DEBUG 1 in it
2) create a blank project then adding an application and a code file, and include the header
3) copy the code from the tutorial(hello world)
At this point, I saw that if I added #if C_DEBUG line, anything after would turn grey(despite being 1), and any code inside won't translate to C++ from Esenthel Script-a lot of stuff still works because EE script is close to C++ and doesn't need to be translated.
However, I found that when I went back to the application properties, cut the existing path, re-pasted, and closed the properties, everything went back to working as expected. When using that method with my project, it started working again. (*phew!*)

Many thanks for reporting the issue!
I've managed to fix this and it will work ok in next release, but if you'll encounter a similar problem in a different scenario, then please let me know

Thank you, sir