The only way to safely make a fan work is for it to be a mod of one of the originating games or otherwise require some data files. Any project that requires an original game--no matter how major a revamp/sequel/etc. it is or how little it uses of the original data--gets a free pass because it isn't an independent work. I have never heard of any fan project that requires base data being shut down, but there are many, many cases of standalone projects being shut down.
If the project doesn't require some official base it is basically only alive for as long as the copyright holder wills it, unless you are lucky enough to get an official blessing (not many ask, however, because they want to get as little official attention as much as possible to avoid being shut down).
LordCinnamon: Can someone explain to me why they don't 'just' remove all references to KQ and continue working on it? (maybe it isn't that simple, I don't know anything about the project or Kings Quest).
Some fan projects do this, others just disappear.