The edit process between author and editor is a delicate balancing act. Each party has the same goal: to make the story the strongest it can be. Yet we approach the goal from different angles. I've heard tales of authors who refuse to let editors change a single word of their work since, real or imagined, their prose is sheer genius and shouldn't be "messed with." On the opposite end of the spectrum are authors who expect an editor to fix every misspelled word, every loose thread in the plotline, etc.
Most of us, though, fall into a middle category. We know our editor is on our side, and we work together. An author must choose her battles wisely: sometimes giving in, sometimes standing her ground. Often, we mourn those scenes we're forced to delete, those scintillating bits of prose that for whatever reason don't work as well as we'd hoped. For me, nowhere does this scenario bear more truth than when a joke or humorous scene fails to gain the right reaction. Stand up comedians often talk about how they hone their craft, night after night. They'll gauge reactions from an early evening show and make improvements or adjustments in a later show that same night. For them, it's about rhythm, about word choice, and about gaining the biggest laugh with the quickest punch.
Writers, however, don't have the luxury of a truly live audience so that if the joke doesn't work in the eight o'clock show, we can't tweak it before the ten o'clock show. We have one chance to get it right. And most of the time, our preview audience consists of a few close friends (who are often too close to the joke) and an editor. So what happens when your editor doesn't get the joke? Should you stand your ground and insist it stays as is because a wider audience might pick up on the humor? Well, you could--if you're like those authors I mention who believe their own press. But sometimes it's better to take a different tack.
Basically, you have two options. The first is to make the joke stronger. Sometimes a new word choice, a quicker journey to the punch, or a new way to tell the same old cliche works. When it does, zing! Pure magic occurs. Sometimes...it doesn't. And when that happens, you're left with Option #2: ditch the joke or scene.
It's a painful decision. But ultimately, they're just words. And if they're not making magic on every page, your reader will walk away unimpressed.