Editing a novel, to quote Miles Rockford, Mission Director of the Needle, is a bit of a headfry.
It's a bit like looking through a telescope while keeping the other eye open - you're looking at part of the picture in detail, observing what makes it brilliant, what needs to change; while the other eye sees the whole of the story, stopping you from deleting something that has to stay for the sake of events elsewhere in the story.
It works the opposite way too; every now and again I have to stop editing the passage on-screen, and scramble to update another part of the story, thousands of words away, so the tumbling, time-travelling life of single mother Penny all makes sense.
It's not easy, and it's taken me a lot of time to discipline myself to make the story work in every direction - thanks to the help of a lot of coffee and a program called yWriter, which I use to organise Hidden Daughter into organisable blocks. It lets me move blocks of story around quickly, helps me keep track of whose point of view each block is written from, lets me store away blocks I don't need (rather than deleting them forever) and because it breaks everything up into little bite-size blocks, my little laptop doesn't break into a sweat as I look for the next thing to edit. It's not perfect, but I found it easier to work with than one big text file. And it's free.
There's lots of other applications on the market, and they've all got their advocates, and I recommend you try out a few to see what works for you (and don't forget to back up EVERYTHING before you start - I don't want a lost manuscript on my conscience). But I know what it's like to be stuck with a huge manuscript, without a clue what to do next; so if my experience is of any help to you, fantastic.
Right, time to open a new folder, and find out what happens to Penny next...