So, since nobody mentioned that, i'll ignore your edits and try to answer your original concern. Generally speaking, this is S-Expressions (as others have said) and S-Expressions are trivial to parse and edit - you can write a parser in C that converts this to a tree easily. Note that the comments and such are a problem regardless of the config syntax used but the solution is the same: instead of rewriting the file, edit it in-place (to do that a simple way is store the index range of each node's value in the code buffer when parsing it and when you modify the node's value update the buffer's contents - make sure you also update the other nodes' ranges if the value changes length in characters).

All these assuming you want to implement the thing yourself. Which is fine, S-Expressions are one of the easiest tree syntaxes to parse. But there are already libraries that can do this for you (including full Lisp/Scheme interpreters) and some of them can even 'pretty format' the code like the quoted snipped above.

So generally speaking this wont be a problem in practice.