The server calculates your points. You do not lose anything if the client crashes on you. It's possible you've lost points for other reasons, problems on the server side of things, but it definitely is not anything you or the client as done, nor is there anything you can do to fix it, other than bringing it to the attention of the Waze team to investigate.
I believe I lost quite a lot of points during the recent holiday contest. I'm around 500,000 right now, but I think I'm missing 30,000-50,000 points. Oh well.