No one wants to talk about this, but the same thing can happen to your novel. The novel you carefully crafted in every detail may in some way be "off level."
Rewriting: the edit-beyond-an-edit. I've done it three times.
A rewrite is a necessity when you've got what's basically a good novel, but it has a structural flaw so deep that you cannot prop up the thing by any other means. The scope of the change is such that it's going to affect every page, if not every line. For example, changing from third person to first person, or present tense to past tense, or changing the setting from Cincinnati to feudal Japan.
When I got back the rights to The Guardian, I discussed my intended changes with my agent. "I just need to move all the commas around," I said. "I didn't know back then what a comma splice was." She said, "That sounds like a pain." And with what Mark Shea calls "hermetically-sealed pride," I replied, "I type really fast. It'll be easy."
In actuality, as I began "moving all the commas around," I discovered that a) I didn't know how to write back when my first novel got published, and b) the commas were the least of the matter. Every single sentence in the book changed. That's not a joke. I realized in rewriting that the message of The Guardian could be summed up as "Emotions are dangerous and hurt people, and the most dangerous and hurtful is love." I realized one of the main characters was a classic codependent, and this was held up as a laudible thing. Worst, I saw that in my authorial intent to help the main character find redemption, I'd given every other character that same goal, when in effect the main character was a murderer and understanding him should be the last goal on everyone's mind.
Rewrite. Time for a huge rewrite.
(I'm sorry my examples are from my own work, but I don't feel comfortable sharing the flaws of others' pre-rewritten books.)
Several years ago, I looked at a book I'd written in when I was 19, and when I finished, I remembered a scene from the "Gorgo" episode of Mystery Science Theater 3000, where a ship has just finished fighting a storm and a monster, and then, after a harrowing moment...it's the next day and they're having smooth sailing. Mike and the 'bots sing to the tune of The Wreck of the Edmund Fitzgerald,
They pulled into port -- everyone was okay!
They went out for lunch and felt better!
(Just a note: being a MSTie has helped immensely with editing my own work. Either I make fun of it or everyone else will. Guess which option I prefer?)
Rewrite. Time for a huge rewrite. Moving scenes, changing motivations, maintaining the danger, having one of the protagonists inadvertently hinder the others -- rewrite.
So how do I recommend you do it?
Don't attempt to this kind of scope with an edit. Begin with a blank document. (Okay, I'm lying: that second one? I rrewrote it by hand.) Print out your entire novel and glance at what you're about to rewrite, then turn away and type it fresh. For any pet sentences you must keep, freewrite to that point and then glance at the sentence and type that, but then look away again.
Here's why: most likely any mistake you made wasn't by accident. You (and I) made those mistakes with full intention because we didn't know at the time not to do it. We probably made a decision to write that novel in that way, and at the time, those decisions appeared correct. Of course I know how to put commas in a sentence. Of course I know what tension is. Of course that's not codependency -- that's sacrificial love. Can you hear me now? Because doubtless I said it back then when I created tension-free comma-spliced codependent novels.
You can't edit that out. Artifacts of your old way of writing are going to stay if you just try to sit the new writing on the old structure. Your novel deserves better than that. Give it a level foundation. Start with a blank document.
As you go through, mark up the old document. Throw out the pages as you finish them, but if there's something you need for later, circle it and save the sheet and place it when the time comes. That scene from the end which makes no sense when the MC is safe but would be heartbreaking when it appears he's going to die? Yank it up front. All that backstory which is so heartbreaking to you and boring to the reader? Use your scissors, cut it up by paragraphs if you have to, and paper-clip it to places later in the manuscript so the reader can enjoy the heartbreak then.
Make every change you have to. Don't leave anything "for later." Know in advance every change you think you'll have to make, and then don't be discouraged when clearing up that problem uncovers a dozen more.
It's worth it. How do I know? Seven Archangels: Annihilation was published in 2008 by the first publisher I submitted to after the rewrite. The Guardian will be re-released at the end of the month as The Wrong Enemy. (One dollar per preorder goes to Heifer International!) And the third one...? It's on submission now. I'll let you know what happens.