That's what I did recently, and it made my novel stronger.
You see, I was writing the second half of my current novel (POP), when I realized that I hadn't really mentioned several of the secondary characters in awhile and was forgetting to weave the secondary plots in with the primary plot action.
So, I began throwing in a paragraph here and there, bringing back the secondary plots and characters. But I soon found that my story was lolling itself into a boring dead end.
Obviously drastic measures were in order.
So, I skimmed through the entire manuscript on the computer and realized that the plot, which had seemed so fabulous when I first outlined it, was really just an uneven batch of little stories that weren't combining to make a very convincing whole. (This is sometimes hard to see when one is zipping along through the middle.) My plot was heavy on action in some spots, heavy on interpersonal interaction in others. Certain characters that were quite important in the beginning disappeared completely for three or more chapters in the middle, then showed back up at the end as if they still belonged there. It was an unorganized circus.
A major change was needed. (And, I must tell you, I HATE changes.)
But, overcoming my fear, I yanked on my overalls, grabbed my printer and a "correction pen" and chose to take control of the circus.
I printed out the entire manuscript, separated each chapter into it's own little paper clipped stack on the floor, and SHUFFLED THE DECK.
Chapters 1, 2 and 3 stayed where they were, but after that everything got shuffled. Chapter 7 became chapter 4, the old 4 became 5, 5 became 6, 8 became 7, 6 became 8, 11 became 9, 9 became 10, and my last 2 chapters got separated into four. The first moment of the change was scary, but after that I felt liberated. It wasn't my words and paragraphs that were bad; not even my plot or characters. It was the order, the clumping, the unevenness that needed to go.
And after the shuffle, my manuscript is stonger. The main and secondary plots flow together like two little streams throughout the book. (Or, so I hope). Characters don't disapper for chapters at a time. And most of the brilliant scenes that I wrote before are still intact. They're just in differente places.
This experience has liberated me. The manuscript was not a lost cause. It was just a deck of characters and scenes in need of shuffling.
So, if you notice plot clumping, disappearing characters, or other uneven fiascos in your current manuscript, don't panic! Don't cut it up and toss it in the trash. It may be that all you need to do is cut the deck -- and shuffle it.