I've done it several times. With GIVING UP THE GHOST, I originally named the high school Richler, but I thought that had too much in common with my actual high school (Riverdale), and since one is not actually based on the other, I decided to change it to something completely different (Frazer). Thankfully I was not married to the name in the first place--it was more of a place holder. I also changed a few last names: Cass McKay sounded too pat, so she became Cass McKenna, for instance.
With THE HALFWAY HERO, the names have changed a lot, because five years ago when I first started thinking about it, it was set in a British-esque society. I was able to keep my main characters pretty much the same (Jared --> Jarad, Cecily --> Sesili) but the character formerly known as Brant is now Deniz. What I found trickiest was finding names that were somewhat foreign sounding and fitting with the cultures I'm playing with, while still looking pronounceable and feeling a little familiar.
Now, as I'm finishing up this rewrite of POSSESSING LUCY, I'm having to make some changes I find particularly hard, because I somehow managed to miss things the first few times I went through the novel. One secondary character shared a name with a secondary character in GUTG (I managed not to realize this until this draft because the characters are so different in personality, and also because it's [name] in GUTG but Officer [name] in PL). So I fixed that. Then my writer's group pointed out to me that my main character and her romantic interest's names may have connotations I'd rather avoid. Lucy and Rick... I LOVE LUCY... Yeah. Somehow that never occurred to me. :P
Lucy is staying Lucy, of course. She has always been Lucy, and she's in the title, after all. But Rick... He's been Rick for a long time. I like the name. I like the way it fits with his sister's (Roz and Rick--they're nicknames for Rosita and Enrique). Nevertheless, I am going to be browsing Hispanic name lists over the next few days to see if I can come up with something I like equally well.
Aren't names fun? *sighs*