Does Vadderung telling Harry that a mortal wizard can't possibly draw enough power to go back in time have any play in the conversation?
according to SmF, the headaches are natural reactions to when someone changes a person's memories. If you recall, harry had his firsts et when mab took his blasting rod.
Actually, as I've been rereading through the series, I've been compiling a headache journal for Harry.
The first time in the series he complains about a headache not related to an injury is in Fool Moon.
However, there's another series of headaches that happen where Harry has a headache, and then does something uncharacteristic. It's most obvious and frequent in Cold Days, but it's also happened in the series for some time, and at least one such occurrence happens in Summer Knight.