First, ouch, I haven't done that, but I have envisioned it many times, every time I carve a neck in fact.
Because I figure it's an eventuality I have thought about what I'd do. Since you're doing a bolt on, I think this is not too difficult to fix, though you'll end up with a unique looking neck (not necessarily in a bad way).
I would make a router sled and support the neck, which won't be super easy considering you've already done the radius on the front (Alternatively you could support it and send it through a sanding planer). Take off enough off the back to almost expose the truss rod. Once you're close use a knife to cut the final bit out and remove the truss rod. Once you have the truss rod out, make the flat spot wide. Take a strip of walnut (or even better a strip made up of both walnut and maple) and cut a corresponding truss rod slot in the strip. Line everything up and glue the walnut strip on, then go back to forming your neck. Lining up that slot in the walnut with the existing slot might be tough, but I think the truss rod should ensure it's lined up.
Let us know what you do though, I'm interested to steal your ideas for when this happens to me.