> Use the mode how exactly? I mean isn't the problem the os.replace()
> call and not os.open() on the source file?

If you want to reproduce the original file's access rights, you have to
pass the right mode flags to os.open().
Of course, this won't recreate symlinks and the like. But I don't think
we can do something for that anyway, since we want to replace to happen
automatically. People who like to have symlinks for their pyc files
probably have their own custom scripts to create pyc files, so they
should just re-use them.