Names tend to stick and sometimes you name your characters for silly reasons. But, what when you hit a certain point in worldbuilding where you realize you want to change most of the characters' names (including the main protagonist) to follow a newfound theme in the story? At first glance doesn't seem much of an issue, but when you think of a certain person as "Mary" for long, it's hard to change, you decide to rename her "Kate" but your brain still thinks of her as "Mary". Is it desirable to change identification of a character late into story development? I referenced names in the thread title but also applies to appearance I believe. Personality is unique and very difficult to change, so let's not get into that.
Well I think this is just a problem for the writer, as s/he is the only one who knows about the previous name. And when it comes to that, I feel its quite personal thing. Some of us don't feel a difference, when someone struggles with the new name. I don't have problem thinking some character with a new name, but I still remember the names I come up with.
I don't think its a big deal to change a (or several) characters name while writing a story. When you are writing, you are discovering more about your character; and if they say "My name is Kate, not Mary", then call them Kate. In my own writing I change the characters names all the time, or I just give them mnemonic names until I find a name that fits.
I don't change character names, even if the one I was originally using was a bit crap. I normally find that once I start writing a character I get a feel for their identity under that name and changing it never sits well with me. I think that it adds an air of truth to the character. Practically no-one gets to choose their name (and many not even their nickname) they just build an identity as whoever they end up being, so having characters with kind boring, normal, non-slick, non-sexy names is actually a nice way to make them fit. Just whatever name comes to mind is fine. I just find my characters make their names their own. You can still play games with names of course. That's one thing I love doing. Different name forms and diminutives and nick names for different people and situations. It helps you create relationships without narrating about them at length; flag who is a friend, who is an acquaintance, who is in charge and who is affectionate. It's nice and works with a lot of names. If a characters given name sounds a bit crap then maybe someone they are close to will come up with a more complimentary nickname for them. So consider sticking with what you had. If she feels like Mary then call her Mary.
Find and replace is your friend! I use names as placeholders all the time, knowing I will change them later. Erzgebirge; do you think I can spell that on the fly? Not a chance, whenever I write, they are simply the Ore Mountains. A lot of times, when naming things on the fly simply so I can keep writing I'll use Native American words. My story takes place in Europe, so all the Native American names stick out like a sore thumb. It makes it easy to spot them when I go back to insert the correct names later.