Why not just do a full, clean build when you hit strange bug? If your workflow is anything like mine, partial-compile and tools like ccache have saved months of hours I would have wasted waiting for the compiler.
That's a big problem with build systems based on timestamps, not checksums. Also, unless the build system can see all the inputs to the compilation, there's the potential for trouble.
That's why Ninja build is so amazing for C/C++. It can use the whole dependencies output from the compiler and knows exactly what to recompile, even if only a header changed.
