limitup, it is actually the all-time CTR for the keyword that matters, with the most recent 1000 impressions being weighted a bit more heavily.
One way to look at it: every single time a keyword has an impression, it's CTR has changed. The same is true if it has both an impression and a click. The AdWords system works on this basis, and weights to most recent 1000 impression more heavily. However, if you have a truly horrible 'most recent 1000', your past history, assuming it is at least reasonably strong, will save you.