flake, our wee girl is just about 24 months and she's been having a really hard time with the shakes too. I've talked to a few different folks about it (a child psychologist, social worker, plunket nurse etc)
The thing that everyone I talked to agreed upon was that while the aftershocks are still happening, the absolute best thing we can do is reassure them. If it means they are in bed with us, so be it, because this whole earthquake thing is traumatic for some kids and is well out of a normal human experience. She is scared, and the hard thing is we can't promise them that there will be no more shakes cuz we just don't know.
Another tip that I found really helpful is trying to make her room a safe place again. Spend extra time in there during the day. Get a new toy like a teddy or book that is just to play/read in her room. A nightlight might give her a bit of comfort too (because the initial quake, and lots of the aftershocks, have been in the dark night when they are alone)
Hang in there, it will pass, and she should slowly get back to normal.

I've noticed that my DD is slowly getting more comfy in her room, though every night that's bad sets her off again (like last night!)