I have this chimera-type character whose name is Ryu, but at this point I think it best to change his name. But I've already grown used to his name, and I've written it all over my book pages. Is it too late to completely change his name?
I would argue that it is never too late to change a character's name, but I think your question is more about changing the nationality of your character. It is one thing to go back through your manuscript and do "replace all" with the names - that's pretty simple, actually. It's another thing entirely to change their background.
For example, I called my MC John starting out but now I think I prefer Jack. This doesn't really pose any consistency issues, because Jack and John both insinuate the same or similar backgrounds. But if I change John to Ryu - suddenly I have completely different preconceptions about his character. I would probably write Ryu differently to John - his experience in life has been different because he comes from a different culture. As much as the world has become homogenised, those cultures are not simply erased.
And if you don't see any difference, why have you made him Japanese in the first place? Why have you made any of your characters the nationalities they are? If none of the names in your story say anything about the characters' backgrounds, having two or more Japanese names would really make little difference to the reading experience. They would simply be names. It could be that that's what your aiming for, but if not it might be good to think more about why you have two Japanese characters, not two Japanese names.
So based on our little comment convo, I would have to say that there is no such thing as "too late". It's just a matter of how much time and effort you want to take to back track and rework the story/character biography. I am not sure if I would be in the minority with this opinion, however, to me names are just as much a part of the bio and personality as everything else. To change the name would mean that you also need to tweak the bio/personality of the person OR find a different name that still fits the character template.
For me, I have been developing several characters for several years now. I wouldn't change the name because the characters are essentially your babies. We don't give birth to children and then at 4 or 5 years old decide to change their names because there are too many Adams in pre-school.
Try giving him a fuller name. You said that he is half Japanese half German. Keep his name as Ryu but expand his name. Since is father is German (typically take on the dad's last name) You can say that his first name is Ryu but then his middle name is Gerhardt and last name is something like Schimdt or some other German name of your picking. You can add maybe some internal conflict that Ryu rejects his Japanese nationality and prefers to go by his middle name of Gerhardt. This way, you add some character arc. Maybe some added side story to why he rejects his first name, still keep him as Ryu while allowing the audience to know that he prefers to go by his middle name and thus changing his name.
I've dealt with this problem, and my answer was "no."
There was a main character in one of my stories that I didn't know what to name, so I just used the name "X." After seeing "X" innumerable times, the name "Xerxes" jumped out at me. It was a good name, not only for the two X's but also for the fact that Xerxes was an ancient king, and this person wanted to be a "king" in America (a corporate CEO actually). So I just expanded all the "X's" to "Xerxes." (Note, this is not the actual name of my character, I'm just using it for illustrative purposes.)
You have a character with Japanese name of "Ryu." Now, you believe you've come to a time to modify the name. There might be take-offs on the name, but one of them might be Ryu Kyu, for "Okinawa." If this is any importance to you, you might want to move in this (or another) direction with the name.
"Ryu" in Japanese sounds like the western "Lo." Two names that come to mind are "Lothario" and "Lohengren."
I'd say change it, you don't need permission.
At first, I was going to ask in comment What is your motivation for changing the name?
But then I realized that did not matter, if you are inclined to change it at this point, then I suspect the existing name doesn't really fit the character for some reason, he doesn't seem like a "Ryu" to you.
I would agree with others that your character needs a name plausible for whatever culture he was born in, but I presume like most cultures I am familiar with, Japanese names seem to evoke certain personalities. This can be used to play against reader expectations, but that can get tiresome for readers. Usually it is better to stick to knitting and give a name that fits their personality. IRL our names can actually influence our personality.
As a discovery writer myself, I may very well change a character's name a quarter way through a story, because they ended up being a different kind of person than what I originally envisioned. As soon as my writing has found what I feel is a "real person", I go through my naming resources and find something better, than rewrite. Not just to change the name, but from the beginning to change their voice, their attitude, humor, word choices, reactions and emotions, to fit with the "real person" I discovered.
I think of this as metaphorically "growing up," IRL our adult self is shaped by our experiences and trials of our youth. For my adult characters at the beginning of the story they have no such experiences, but as the story progresses I see how they must react (by my logic) to fill their role correctly.
In your position, for example, I may know Ryu is a chimera, but it was not until I put a chimera into conflicts, relationships, family and perhaps romantic situations, and thinking through what a chimera "would really do" in such circumstances, that I see how his personality would have adapted to his abilities, his sense of humor, and how he sees the world. I find some plausible consistency in that, and Okay, then I have a real person, and now (on behalf of the reader) I want a name that better implies his personality.
I believe that this is no problem.
If you don't like his current name, then would it not surely be easier to switch to a better one and start using it?
I think that if 'Ryu' holds special symbolism within the book, perhaps you should keep it, however if there is a definitely better different option available, go ahead and switch!
For me myself, I actually have had a situation in my own writing where in book 3 out of 3 I decided to change the name of one of the most instrumental characters in the trilogy. The name she holds now has much more meaning for her and is a far better pick. It was a good decision to have made.
Ultimately, it's up to you.
Names are variables. They are identifiers, not what is under-neath. There are some names which do become entwined in the understanding of who a person is; and so changing the name might remember clean-up.
The quick answer is that: No, it is never too late to change a name. Find & Replace can do this quickly in any word processor. Or, as you transcribe a written copy into a computer, you can manually make the adjustment.
Right now, the answer for you is likely that until your story is done, if you can ignore it and know you will change it later, you should wait. Names are relatively inconsequential things; in the grand scheme of your story, "a Rose is still a Rose by any other name". If the name is too much of a distraction, then change it; or, find a way to grow and be complacent with changing it once you are done and sure your story requires it. It is a quick fix and, at the same time, a quicksand-trap ala world building.
You have to choose how your time is best spent, and I would argue that finishing your story first is more important than the name of a character.