This isn't applicable to scheme as a config format, but some config formats are line based and have programmatic tools to manipulate them, e.g. the .ini-like format Git uses, try adding some comments to ~/.gitconfig and manipulating it with `git config --global <...>`, it'll all be preserved.

You will lose any comments like this though:

    [user]
        name = My Name ; that's my name!

Programming is hard in the face of arbitrary user data.