I've recently had an agent request the first 50 pages of my manuscript after being "intrigued" by my query and first 5 pages. Good news, for sure. Here's the thing: a MAJOR plot development happens on page 60; a real WOW moment (at least I hope).
I didn't press my luck. I submitted the first 50 as requested. But I really wrestled with the idea of emailing the agent and letting her know about the major plot development and asking if it would be okay to send the first 60 as opposed to just the first 50. Would that have been okay? Or did I do the right thing but just giving her what she asked for and not pushing it (even though it would have potentially meant she'd have gotten to experience a real juicy moment)?
What you didn't understand (and not cause you're stupid, but cause you're not sitting on my side of the desk) is that "the first 50 pages" really means: don't send the whole thing but let me get a better sense of the book than those first couple pages.
In other words, if you have a major plot development at page 60, send 60 pages.
The agent wants to find work she can sell, and major plot developments are often a reliable indicator of just that.
Querying is not engineering. You don't get extra points for sending exactly 50 pages and no more.
While, yes, you hear agents moan "please follow the directions" what they mean is "don't send a PDF when I need a word .doc"
If I were in your shoes, I'd email her and say "yanno Snookums, there's a major plot development at page 60 so I've sent you that as well as that earlier email with just the 50."
Honestly, if she lambastes you, you'll have some good info about her communication style which might actually be more valuable than you know.
Understanding WHY this is a rule will help you know when you can break it. It's a rule so that authors don't send the whole manuscript. It's also a holdover from when everything arrived on paper and mailing 50 pages was less expensive than all 300+
But knowing that, you send 60 pages and NOT the whole manuscript because you know what she's really asking for.
Be super careful about knowing what agents really want. It's best to follow the directions as exactly as you can, but still, look at the bigger picture when you face a question like this.