Ah, I get it. If we remove points from [itex]C[/itex], those points may remain discontinuity points of the indicator function of the reduced set. Since every point in [itex]C[/itex] is a limit point of both [itex]C[/itex] and not-[itex]C[/itex], that point will be a discontinuity point of the indicator function even if it is taken out of [itex]C[/itex]. For instance 0 is in [itex]C[/itex], 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 [itex]C[/itex] and not-[itex]C[/itex] respectively and both have limit 0. So the set [itex]C-\{0\}[/itex] 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 [itex]\Rightarrow[/itex]s from post #96.
We prove that any countable union of closed sets (ie [itex]F_\sigma[/itex] set) is a Borel set. Since [itex]\mathscr B[/itex] is closed under countable unions, it suffices to prove that any closed set [itex]S[/itex] is Borel. The complement [itex]S^c[/itex] is open and hence every point [itex]x\in S_c[/itex] is interior, meaning it is contained in an open interval that is fully within [itex]S^c[/itex]. There is a largest path-connected component of [itex]S^c[/itex] containing [itex]x[/itex] that is the open interval [itex](a,b)[/itex] where [itex]a=\inf\{y\in\mathbb R\ |\ (y,x]\subseteq S^c\}[/itex] and [itex]{b=\sup\{y\in\mathbb R\ |\ [x,y)\subseteq S^c\}}[/itex]. [itex]S^c[/itex] 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 [itex]S^c=\bigcup_{n\in\mathbb N} I_n[/itex] where the [itex]I_n[/itex] 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 [itex]F_\sigma[/itex].