If it's a good copyeditor, most of the red marks will have nothing to do with us....the copyeditor's job is to mark the manuscript for the typesetter, so that things we can't do (or shouldn't do) on the computer are made clear: which set of all-caps should be small caps, which line break is just a line break and which gets a little squiggly bit of decorative stuff in it, what size the chapter heads should be, and so on. The writer's eye glides easily over the page when all the red marks are that sort of red mark.
But those others--! Copyeditors also have authority to mark for correction our misspellings (the wail of "But I checked it four times!" goes unheard by the copyeditor...if there's a "teh" left, they're supposed to find it and mark it.) If there's a missing set of quotation marks you didn't notice...if you ended a sentence with a comma and not a period, if there's a space missing between words...all those typo-related things. Well...that's not too bad, if they get them all right. But then...then the famous treading on authorial toes begins.
Did you use the same word twice in the same paragraph (or even, nearby paragraphs?) That's an "echo" and the CE will mark it and may even be bold enough to pencil in his/her idea of a good substitute. Sometimes the CE fixes one echo only to create another. Or sometimes the suggested word is wrong--in meaning, in tone, in sound (for instance, creates a row of long-i sounds, or has too many syllables and breaks the flow.) Unintentional echoes should, of course, be dealt with...but most of the time, in my experience, the CE's suggestion isn't the best.
CEs seem to be the last line of junior high grammarian defense against standard usage on things like expletives in dialogue (they want it all spelled out properly: Damn it, not Dammit...which, by the way, is read differently and *feels* different.) They are particularly strict on word division, combination, and hyphenation, even when the words in question were created for a science fiction universe set in a galaxy far, far away and centuries hence. They insist on inserting unnecessary (easily understood by the average reader) relative pronouns, so sentences begin to sound like something designed for sentence diagram exercises. They want to flatten all to the current standard for American business, which is, for a fiction writer, pretty damn (they want damned) flat.
The bad CEs (not the one I'm currently dealing with, but last year's, and another one who gave a friend fits this year) decide to rewrite the book, changing words, phrases, and punctuation (and sometimes characters and action) with a lavish disregard for whose name is on the cover of said book.
It is the writer's job to return the copyedited manuscript in a tearing hurry and in a form clearly understandable by the typesetter. The "stet" should line up with what you're stetting; the underline for the "leave this alone"section needs to be obvious. But if the CE has written all over that line, offering corrections of dubious worth, and filled the margins with a long explanation of why he/she made that change...where the !**@! are you supposed to put the "stet"? (You aren't supposed to erase the CE's marks...the entire history of marks should be visible to the typesetter, I've been told.)
I don't mind if CEs question something...a neat red question mark with one or two words is fine. I would rather have the question mark than a suggested correction. Let *me* decide which of the echoed words should be changed, and to what. I don't mind if the CEs mark an inconsistency (in fact, I'm glad it was caught) but again I would prefer a question mark, a short (not paragraph long) explanation, and the chance to fix it myself, so I'm not trying to write even tinier in blue or green pencil (only the CE gets to use red pencil and nobody uses ink) in and around the red stuff. I would like CEs to realize that a lot of people have read this before they have, and the main editing and line editing have already been done. It's not their job to fix what they think are plot problems, because those aren't plot problems: those are problems caused by reading like a CE (which they're supposed to do) and not like a reader. Particularly in SF/fantasy, where the world the writer is creating for the reader may be far from 21st century everyday, the CE should be wary of idly changing words, phrases, capitalization, etc. All we writers have, to create these strangenesses, are the words we use and the order in which we use them. Every word either sharpens or blurs the focus we're trying to create. No one expects the CE to "get the vision"....but CEs need to know that the vision exists, that they don't get it, and thus they should tread warily (use the question mark, rather than crossing out a word and writing in their own.)
The writer who raises a stink about a CE is always at risk of being considered a problem child, someone hard to work with. Unless the CE has been very bad indeed, the writer's protest that the CE's correction ruined the feel or the flow may be seen as fussy and arbitrary. So the writer faced with a lot of copyedited manuscript to get through in the typically short time allowed (because at this stage the writer does not have the option of taking a few more days to work on it--the book is on a production schedule and must arrive at the typesetter's on time) may be tempted to give up and let it all go.
That's a mistake. Whose name is on the cover of the book? Not the copyeditor's. Whose style is going to be savaged by reviewers? Not the copyeditor's. In fact, the average reader will never know who the copyeditor was (many times, neither does the writer), or what the copyeditor did, or even that changes made by the writer can be un-made in production (it happens. I'm not the only writer who's discovered that an earlier draft was used instead of the final one. For me, only once.)
So the copyedited manuscript is...a strain in the life of every writer, no matter how good the CE is this time, and the memory of the horrors another time never really disappears.
And again, ritual disclaimer, the one I'm working through now is not that bad.