I read this book some time in the mid-2000s. I'm pretty sure the author's name began with R.
The main character is a (probably teenaged) boy who encounters a strange girl at his school and subsequently begins to 'disappear' from his own life. It's an effect similar to that in Neil Gaiman's Neverwhere: people look straight through him and don't realise he's there, he vanishes out of old family photos, and so on. I think his (probably younger) sister remembers him for longer than his parents or anyone else, but eventually it's only the strange girl who acknowledges his existence.
She turns out to be an agent in an organisation who use time travel to sort out 'mistakes' in time. I believe her messing about to prove to him that she had time travel powers was what caused him to disappear: she went back in time to pop up in an 80-year-old photo from one of his school books, but her pushing someone else out of the photo ultimately led to a change in the course of the Second World War and the untimely death of our hero's grandfather.
There's also a typical villain character: creepy and powerful, dressed in a black cape, with some ominous name like 'Midnight' or 'Darkness', he commands a swarm of gargoyle-like creatures and has the ability to stop time (he once conducts a whole conversation with our hero in between the eleventh and twelfth chimes of the clock).
Much of the story revolves around trying to undo the damage this girl agent did to history, and contending with this villain in order to do so. It was only the first book of a series, but I never got any of the others. (I think I read a sneak preview of the second book, which may have had something to do with Shakespeare, but don't take my word for it.)
If I had to guess, I'd say the two main characters were called Jamie and Anna, but again I'm unsure.
I've hunted around a bit online for this book but couldn't find it. Does anyone else know what book I'm talking about?