This is a subject which came up indirectly in conversation with a regular client recently, and sometimes I know can worry authors without much experience of the structural editing - not copyediting; tidying text is never that challenging - process: You’ve said you think I should change X and Y and rewrite Z, but isn’t that a lot? Does this mean my story’s no good?
This is a particular concern with novels - you’ve spent maybe months writing something only to have your editor tell you (sometimes at length) that they think it’d be better and stronger if you cut or changed chapters, scrubbed scenes, reworked characters. As a writer, it can seem like you’re looking at junking tens of thousands of words (and occasionally that’s absolutely correct) and so weeks of effort. No matter how constructive they’re being - I and any good editor will be constructive, offering explanations as to why they think changes are needed and suggesting routes to doing so, particularly ones that will mean minimal actual rewriting - it’s natural to feel your confidence take a hit.
But while “normal” is a moving target in this respect - apart from anything else, many writers “edit down” and most changes are cuts, while others “edit up” and most changes mean fresh additions - it’s perfectly common, even in writers with years of experience and a truckload of published work behind them, for a first draft to need sweeping changes. The yardstick I always turn to is my fifth published book (and ninth written), for which to satisfy my agent I needed to rewrite half of it, one of the two main POV characters, twice, the first time basically from scratch. “It’s good, John, but it doesn’t belong in this book at all.” (And then, for my editor, I had to write a new ending, again from scratch.)
On long work in particular it’s very easy to lose an original thread or to fill out a story with cool new ideas that occurred to you partway through but which never quite mesh with everything else. And by the end, with days and weeks and months of work behind you - with all the sunk costs and mental filling-in that entails - it’s naturally hard to see why not all of those things hang together, or that yes, that new idea is cool - so cool, in fact, that it should’ve been brought in earlier and made more of.
The worry is less, in my experience, on short stories, even if the relative amount of tweaking and rewriting can be the same. At shorter length, stories hinge much more on their initial concept and setup; if those are solid, you can feel confident you’re onto a good thing even if the framing or structure aren’t quite there yet, and it hasn’t taken you so long to put it all together that you’ve forgotten that hey, my ideas here were great and so don’t need to feel down about what it’ll take to polish them up.
As a freelance editor for novels or short stories, more so than an editor working in-house where your company’s commercial and list-management needs have to be considered (not to mention where the power dynamic is different; as a freelancer, you’re paying me to make sure your work’s as good as it can be - I’m not paying you to give me something good enough to sell to the general public), good editing is about helping you accentuate what’s good in your writing, avoiding mistakes or pitfalls in the future, and bringing any weaknesses you have up to par with your strengths.
Writing a novel or a short story in the first place is the hard part, and you’ve done that. The marble sculpture that is your first draft might be a little rougher than others, or might have some extra decoration it doesn’t need - or be lacking an element that’d bring it to life - but it’s extremely rare, in my experience, for a piece of work to be fundamentally flawed in a way that this kind of worry is justified. And even then, it’s rarer still that it can’t then be fixed and you won’t come out of it a better writer, feeling good about your work.