Ah, I get it. If we remove points from C, those points may remain discontinuity points of the indicator function of the reduced set. Since every point in C is a limit point of both C and not-C, that point will be a discontinuity point of the indicator function even if it is taken out of C. For instance 0 is in C, and the sequences, written in ternary form:
$$0.2,0.02,0.002,0.0002,...$$
and
$$0.11,0.011,0.0011,0.00011,0.000011,...$$
are in C and not-C respectively and both have limit 0. So the set C-\{0\} is not the discontinuity set of its indicator function, because 0 remains a discontinuity point of that indicator function.
Surprising, and intriguing.
Now, I have managed to prove the second of the two \Rightarrows from post #96.
We prove that any countable union of closed sets (ie F_\sigma set) is a Borel set. Since \mathscr B is closed under countable unions, it suffices to prove that any closed set S is Borel. The complement S^c is open and hence every point x\in S_c is interior, meaning it is contained in an open interval that is fully within S^c. There is a largest path-connected component of S^c containing x that is the open interval (a,b) where a=\inf\{y\in\mathbb R\ |\ (y,x]\subseteq S^c\} and {b=\sup\{y\in\mathbb R\ |\ [x,y)\subseteq S^c\}}. S^c is a disjoint union of such components, of which there can only be a countable number, because every interval will contain a rational number and the rational numbers are countable. So S^c=\bigcup_{n\in\mathbb N} I_n where the I_n are disjoint, open real intervals. Hence
$$S=(S^c)^c=\left(\bigcup_{n\in\mathbb N} I_n\right)^c$$
which, being the complement of a countable union of intervals, is Borel.
It remains to prove that any discontinuity set of a function with domain [0,1] is F_\sigma.