ImageBuilder; Cannot upgrade OS running on eMMC

The MAC issue is solved;

Is there a bug in the ImageBuilder?
I just found this out. I'm using files/ to store my own custom settings etc and I've noticed that when I build, a new file I put there gets removed if I run make clean and make dirclean before building a profile.

I don't recall any files in files/ being removed when running those commands first and I've used IB hundreds of times.