That was an error on my part, the C&D letter was for using the term "App store" not "appstore".
But to answer your question, no they where using "App store" and never stopped using it. I don't know what ever became of the case, if it is still going on or has been suspended.
Here is more of GetJar's rebuttal.
GetJar has been using the term “App Store” in press releases and in it’s positioning with consumers, trade, analysts and press since early 2009 and it’s only now that Apple has decided to send us a C&D. That said, GetJar does not use the term in it’s brand/slogan or strapline. (more...)
It seems they started formally using the term "App store" after Apple created their app store.
Funny in my mind I always considered GetJar an app store since they packaged Java "apps".